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Start Screen for PeakStrainer
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![App Main page](/uploads/efa36b03cbd48d4074ae82e7a40514ac/Capture.PNG)
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On this screen you can select the .raw files by using the **browse **button.
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You can also choose if [Reorder Scans](ReorderScans) will appear after PeakStrianer is finished
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Startup Screen for [Reorder Scans](Reorder-Scans)
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You can also start **reorder scans** without selecting a file or running PeakStrainer
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![Capture1](/uploads/3c5b2b60148c1af927a578fa07e4ad6a/Capture1.PNG)
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![App Main page](/uploads/efa36b03cbd48d4074ae82e7a40514ac/Capture.PNG)
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Choose "other" output options
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... | ... | @@ -57,11 +47,19 @@ if they are adjacent to a group that is above the threshold, this is done to avo |
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Bin Type
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PeakStrainer groups peaks across multiple scans, but the peak m/z may not be exactly the same across multiple scans, therefore we allow a certain range to be considered the same peak m/z, we call this range a bin.
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The size of the bin, in other words the range of m/z values that are considered the same, is variable throughout the full m/z range; usually smaller for low m/z values and larger for high m/z values.
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There are two approaches to determine the bin size at a certain m/z value. One is to take the measured resolution of the peaks at full width half maximum FWHM and calculate the trend function trough the full m/z range, we then use the function to determine the bin size. The other approach is to provide personalized function parameters for MS1 and MS2 respectvely, this allows for more fine grained handling of the data.
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Bins are created based on peaks m/z values, therefore some bins might overlap with one another, you can choose to merge the overlapping bins into one larger bin, that may have a higher peak count, therefore a higher repetition rate.
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![Capture6](/uploads/a34aab2992b3c68bd4770e92f5906e0c/Capture6.PNG)
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Repetition Rate
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Once we have removed signals that do not repeat, in the prefilter stage, and we have grouped signals that are the same in the binning stage, now we can discard signals that are not repeated often enough throughout scans. The threshold for how often the signal must repeat throughout scans is given as a percentage of all the scans, ie Minimum repetition rate.
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![Capture7](/uploads/83cececcd09aaafc540fa350b0334896/Capture7.PNG)
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... | ... | @@ -71,7 +69,7 @@ Status Page |
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When the finish button is pressed you will go to the status page, here some text information is presented to show how the progress of the process.
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If there are problems they will be reported here
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If a problem occurs it will be reported here.
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![Capture8](/uploads/6f418e6e06f18a7091cc70800f65f99a/Capture8.PNG)
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