Package: pymacroms
pyMacroMSHigh performance quantification of complex high resolution polymer mass spectraThe purpose of this program is to identify and quantify macromolecular species
in high resolution mass spectra based on the used monomer(s), possible end-groups
and the adduct ion. Experimental spectra are imported as a centroided peaklist
from a comma-separated values (csv) file or directly from a Thermo RAW file (from v1.0.0). Please find code for example usage
on ourwebpage.From version 1.0.0, pyMacroMS requires a 64-bit version of Python.DependenciespyMacroMS requires the following modules to be installed:IsoSpecPyfor the generation of isotopic patternsnumpy and pandas for data processingsklearn for quantification via linear regressionmatplotlib for quick representation of resultsprogressbar2 for feedback during the more time consuming stepsreportlab and svglib for the generation of a PDF reportpythonnet for the interface with Thermo's RawFileReaderCitationPlease refer to our publication for more details about the algorithm and
cite us when using pyMacroMS in your work:K. De Bruycker, T. Krappitz, C. Barner-Kowollik,ACS Macro Lett.2018, 1443-1447.LicensepyMacroMS is available free of charge under an MIT License.
See the LICENCE file for more details.pyMacroMS uses the RawFileReader reading tool. Copyright Â© 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
If you use pyMacroMS, you agree to the license agreement of RawFileReader, of which a copy is provided when installing pyMacroMS.Changelog1.1.7Now works with IsoSpecPy 2.x, tested with 2.1.4, but does not work with IsoSpecPy 1.x any more. Special thanks to the developers, Mateusz Lacki and Michal Startek, for their help with the implementation.Further speed improvementsMinor bugfixes1.1.0Speed improvements for assembling the possible monomer combinations in the polymer simulation.
Special thanks to Matthieu Soete for sharing his insights.Preparations for a GUI1.0.9Introduced basic support for Scan Filters (limit the imported data to 1 type of scan). Different scan types are detrimental for the averaging algorithm and probably don't make much sense anyway (?)Increase compatibility with Unix systems, installation of pythonnet package seems to be the major struggle thoughMSData class now takes the argument mzOffset, an offset that is added to every m/z value when reading the spectrum.Speed improvements for a large amount of possible compositionsMinor bugfixes1.0.0Thermo RAW files can now be used as input without any pre-processingBy default, all scans are imported separatelyScans can be averaged by providing a range of scans or retention timesNew MSData class introducedHandles reading of csv files (previously Spectrum class) and Thermo RAW filesStores all imported spectra and corresponding processed results to allow for batch processing of multiple scansPost-processing of results still in Spectrum class, so on a per-scan base... Future problemVersion 1.0.0 and onwards are licensed under an MIT License (rather than a GNU GPL v3.0 for older versions) to comply with the license requirements of Thermo's RawFileReader0.2.0Isobaric species are now pre-filtered, which leads to a significantly improved calculation timeIntroduced the option to define a custom database of monomers/endgroups (with a higher priority than the built-in database)Introduced the option to save the output as a PDF report0.1.2Update code to use the new IsoSpecPy 1.9.X API0.1.1Minor fixes to the interfacing with IsoSpecPyFixed compatibility with IsoSpecPy 1.9.X0.1.0Initial release