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PeakStrainer
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=============
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PeakStrainer is a tool to reduce the file size of MS spectra,
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PeakStrainer is an implementation of the paper [Intensity-Independent Noise Filtering in FT MS and FT MS/MS Spectra for Shotgun Lipidomics](http://pubs.acs.org/doi/abs/10.1021/acs.analchem.7b00794).
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It is a tool to reduce the file size of MS spectra,
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it does this by removing signals that do not repeat,
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or do not repeat often enough, between spectra.
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... | ... | @@ -20,31 +21,29 @@ called repetition rate, given as percentage of total max repetitions. |
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The input to the application is a *.raw files and the output at intermediate stages are *.CSV
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and final results are stored as *.mzXML files.
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There are three ways you can use PeakStrainer,
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* The desktop version
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* The command line version
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* The Source code version
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The desktop version is tuned to work with
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the default values that should work well most of the time.
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More options and parameters are available in the command line version,
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the command line version was made for some custom procedures.
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The source code is annotated and should be maintainable and extensible by software developers. The objective of using the source code is to extend and/or improve the functionality of PeakStrainer. Please share any improvements or extensions to the system.
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Reference
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-----------
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If you use the software for a publication
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Please use DOI [10.17617/1.47](https://doi.org/10.17617/1.47)
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as a reference.
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Please use DOI [10.17617/1.47](https://doi.org/10.17617/1.47) as a reference.
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if you would like to reference the paper please use DOI [10.1021/acs.analchem.7b00794](http://pubs.acs.org/doi/abs/10.1021/acs.analchem.7b00794)
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If you would like to share your process and or data, please feel free to provide the data in the [Issues](https://git.mpi-cbg.de/labShevchenko/PeakStrainer/issues) page and we find a place for it in the wiki
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If you would like to share your process and or data,
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please feel free to provide the data in the [Issues](https://git.mpi-cbg.de/labShevchenko/PeakStrainer/issues) page and we will find a place for it in the wiki.
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Quick Start
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-----------
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- Download [PeakStrainer.zip](https://git.mpi-cbg.de/labShevchenko/PeakStrainer/blob/master/dist/peakStrainerApp.zip)
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- Unzip the file
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- run ```peakStrainerApp.bat```
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- select one or more *.raw files
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- click finish to process with default settings
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After processing *.mzXML files will be created in the same directory as the *.raw files
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Disclaimer
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-----------
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Despite all efforts that have been put into the development and testing, the software may contain errors or bugs. Therefore we provide no warranty and assume no responsibility for any consequences caused by the program installation and use. Please use it at your own risk
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License
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--------
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This program is a free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation. See the file LICENSE for details.
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... | ... | @@ -52,3 +51,24 @@ This program is a free software; you can redistribute it and/or modify it under |
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Contact
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--------
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Please contact us over the [Issues](https://git.mpi-cbg.de/labShevchenko/PeakStrainer/issues), It is open for questions and suggestions and other issues related to the software.
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Using PeakStrainer
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=================
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You can use Peak Strainer as an application,
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from the command line or from the source code.
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There are several steps in the peak strainer process,
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and there are several approaches to complete these steps.
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The GUI application is geared toward simplicity,
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only the best or most straight-forward approaches are available in the application.
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The command line is intended to be used in automated batch processes,
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it has the same functionality as the GUI application.
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The source code is available and is intended to be readable and extensible.
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For more about the command line and source code,
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please go to [implementation Notes](Implementation_notes) |