In this section we describe how to use the command line and source code of Peak Strainer. A complete installation, not the single file installation, is required to run command line or source code.
Command line Application
Do to limitations in resources the command line version has not been fully tested.
To run Peak Strainer with default settings from the command line:
To run Peak Strainer with custom settings go to the utils folder and
msps.py -h to display a list of available flags and options.
Because of the complexity of the options from the command line,
we recommend to customize the code in
peakStrainer.py instead of settings all the flags from the command line version.
To review the source code we recommend to start in the main method of the
The code should be readable and you can change it to your setting.
In case the source code documentation seems outdated, please trigger an update as described in Improvements
A simple way to reduce the size of the file is by removing some scans. Scan can be removed based on:
- Retention time, ie from ... to ... in seconds
- By filterline text, filterline is a short text that describes the scan,
ie. filter line should include the text
NSIor filter line should exclude the text
- By Sample, this is mainly for testing, you can get 1 out of every N scans, ie. take 1 out of every 10 scans
At this stage we remove what seems to be random noise. first we combine the spectra that has the same preconditions, ie. mode, selected ion m/z, etc. And we count the peaks at a given m/z value, if the count is very low, like 1 or 2, as compared to other peak counts, then we consider those peaks random and discard them.
This step makes the most difference and facilitates the following steps
Now that we have peaks that can be combined, we try to combine them. First we decide what peaks go together, to do this we use bins. bins give us the lower and upper bounds of m/z, all the peaks within those bound go together in a bin.
Some ways to make bins are:
- by decimal places, if the peaks are close enough... to a given decimal place, then they are in the same bin.
- by measure resolution, given the raw file we read the peak resolution and make the bin as wide as the resolution, ie, peak width at 50% intensity
- by a resolution function, in some cases the measured resolution is inconsistent, some peaks may be very wide or too narrow, so instead we extract a trendline for the resolution and use the trend instead of the measured value
- by resolution function, in case we cannot extract the resolution trendline we can just input function values to estimate the resolution, this way we get bins that grow or shrink across the m/z range
Now that we defined the bins, we need to sort the peaks into the bins, this would be trivial if the bins did not overlap, but sometimes they do overlap so we need to decide how to handle it.
Peak in first bin the matched, quick and straight forward, works well if there is no bin overlap
Peak in narrowest bin, this maintains peak resolution and underlying peaks can be detected, but it is computationally expensive and provides very small differences
Peak in bin sort window, in this case we only check a few bins to see if the peak matches, it is less computationally expensive, than the others
By grouping peaks together into bins we can count how often peaks occur in a given m/z range. We would expect these groups to have approximately the same number of peaks. if the peaks are much less than expected then we filter those groups out
We can see the results of each step in the process trough csv files. there are comma separated values files, and also a psudo mzXML file.