Several modules and tools for protein sequence handling and mass spectrum interpretation
Program mMass presents an open source multi-platform package of simple tools for mass spectrometric data analysis.
The mMass application consists in several modules and tools for protein sequence handling and mass spectrum interpretation with focus on common proteomic tasks.
Here are some key features of "mMass":
Multiple Format Support:
· mMass supports several mass spectrometry formats, such as mzData and mzXML. Mass spectra or peaklist data can also be easily imported from simple ASCII files consisting of two columns (m/z values and intensity values) separated by a tab, space, comma or semicolon. In addition, there is a support for native data from Bruker Daltonic Flex Series instruments.
· One of the popular features of mMass is the ability to open a blank document and create peaklist manually. This feature is particularly useful in those cases where spectrum image or printed list of labelled peaks is available only.
· Finally, there are processing functions such as automatic peak picking, deisotoping, baseline correction and smoothing.
· Two methods are available for data recalibration. Internal Calibration is the classic calibration method, using internal reference values. 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 available for peptide mass spectra. For both methods, either linear or quadratic fitting can be used.
· mMass provides an internal Sequence Editor, which can be used to make any protein or peptide sequence available to other modules. Any modification can be applied either as fixed or variable. Protein Digest tool can be used to generate a list of peptides resulting from in silico enzymatic or chemical digestion of specified protein sequence. Similarly, Peptide Fragmentation tool generates a list of common peptide fragments. In both cases, all possible combinations of variable modifications are calculated and result can be easily compared with measured data. In addition, sequence can be searched for a specific peptide mass by Sequence Search tool to identify non-specific cleavage etc.
· Mass Calculator tool can be used to simulate isotopic pattern of given formula and generated profile spectrum can be easily compared with real data.
· Compound Search tool can be used to search for any user-specified compound in the spectrum. Every compound is specified as molecular formula, therefore both monoisotopic or average mass can be search with any charge. In addition some adducts can be searched as well.
· The interpretation of mass spectra typically involves a seemingly never-ending check of the differences between all peaks in a spectrum. However the Peak Differences tool 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 or specified mass value.
· Although mass spectrometry is a very popular tool for protein identification, it would not be possible without the tools publicly available on-line. 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.
What's New in This Release: [ read full changelog ]
· Internal server has been disabled for OS X.
· An issue with crashing plot canvas.
· An issue with crashing Envelope Fit tool.