mzmine website
MZmine 2 is an open-source framework for processing, visualization and analysis of mass spectrometry based molecular profile data. It is based on the original MZmine toolbox described in 2006 Bioinformatics publication.
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Review of: An Evolving Computational Platform for Biological Mass Spectrometry: Work-flows, Statistics and Data Mining with MASSyPup64
Getting a large number of packages to work together on a single operating system is a daunting task. Configuring specific compilers, interpreters, and organization of permissions is often not achievable by typical scientists. The evolution of MassyPup64 is an important development to encourage distribution of tools that can seemlessly work together.
Recommended revisions:
Original data is almost always in a proprietary format from a vendor. Elaborate on line 44 which formats are compatible with msconvert via the MassyPup64 Linux distribution and which are not. Its my naieve understanding that certain vendors have released their dlls in such a way that they are compatible with Wine and other Linux .net emulators. This is an excellent opportunity to identify the current state of affairs for raw data import for each vendor.
imzml/ibd files are mentioned in figure 1, but there is no mention of mass spectrometry imaging other than line 234 "MSI.R for evaluating MSI data." There are numerous software packages for processing imzml, and they aren't mentioned. This should be corrected unless there is a reason that they can't be installed on MassyPup64?
Python is mentioned briefly on line 205 and there is absolutely no mention of the IPython interface. Including the Python packages for mass spectrometry, computational chemistry, and scientific computing packages needed for plotting, statistics, and file import/export seems like a major oversight that could be easily overcome.
It isn't clear from reading the manuscript if an MSMS reference database (ie: from mass bank or Metlin) and a search algorithm for comparing a measured MSMS spectrum to a reference database is included.
It isn't clear if mzmine is included in this release. For example, mzmine is mentioned on line 162. Is it included? Is Java included? Is the java version compatible with other java apps in MassyPupp64?
My general impression is that many valuable tools are bundled together in this linux distribution, but the style and organization of the paper in its current form makes it very difficult to tell exactly what is included and what it can be used for. A full page table listing the software included would make this much clearer.
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