Commit 3d3aa81b authored by mirandaa's avatar mirandaa
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doc: update

parent b01782be
PeakStrainer
=============
PeakStrainer is a tool to reduce the size of MS spectra,
with the goal of removing inconsistent signals
and combining
PeakStrainer is a tool to reduce the file size of MS spectra,
it does this by removing signals that do not repeat,
or do not repeat often enough, between spectra.
the consistent signals.
To define if a signal repeats we first define a threshold of signal similarity.
similarity is based on scan settings, the settings must be the same, and m/z proximity.
To illustrate consider two scans A and B, both have the same settings.
Scan A contains a peak at m/z 123.0001 and scan B contains a peak at m/z 123.0002,
if the threshold is set to 0.0001, then the peak m/z 123.0001 is considered repeated between scans.
The threshold is adaptable across the m/z range of the scans
and can be estimated based on the peak-resolutions given as full width half maximum (FWHM).
Peak repetition information is used to filter out peaks that are not repeated more than a preset threshold,
called repetition rate, given as percentage of total max repetitions.
The input to the application is a *.raw files and the output at intermediate stages are *.CSV
and final results are stored as *.mzXML files.
Quick Start
-----------
- Download [PeakStrainer.zip](https://git.mpi-cbg.de/labShevchenko/PeakStrainer/blob/master/dist/peakStrainerApp.zip)
- Unzip the file
- run ```peakStrainerApp.bat```
- run ```peakStrainerApp.bat```
- select one or more *.raw files
- click finish to process with default settings
After processing *.mzXML files will be created in the same directory as the *.raw files
Desktop Application
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