Manual

Here we describe some of the options that are available in the PeakStrainer Application.

Start Screen for PeakStrainer

On this screen you can select the .raw files by using the browse button.
You can also choose if Reorder Scans will appear after PeakStrianer is finished

Choose "other" output options

You can get the intermediate files that show how the data was processed by selecting the CSV output, if the output directory is empty the files will be created in the same directory as the selected files.

You can also set the logging, to show any issues relevant information, the log file is useful to fix bugs in the program, a high log level means that most if not all messages are stored, alternately a low log level indicates only the most important data will be reported

Filter out some scans

You can select some of the scans to be omitted from the process, by retention time, or by some text in the filterline.

For retention time, If you leave the start or end field empty it is considered the start or end of the scans respectively.

For Filterline text keep in mind that this includes empty spaces, so for example if I select the text ''ms'' the results may contain ''ms'' or ''ms2'', but if I select ''ms '' (notice the space at the end) then only ''ms'' will appear.

Prefilter Peaks

The prefilter process we remove many signals that are not repeated at all, this steps helps process the information much faster.

To find out if they do repeat we group the peaks by their m/z value, rounded to a given decimal place, then we count how many peaks have the same rounded m/z value. This way we can discard the groups below a certain threshold.

We should note that some groups below the threshold can still be kept, if they are adjacent to a group that is above the threshold, this is done to avoid discarding groups that may have been split by the rounding value.

Bin Type

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.

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.

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 troughout 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 respectively, this allows for more fine grained handling of the data.

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.

Repetition Rate

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 maximum repetition rate, called the Minimum repetition rate.

Status Page

When the finish button is pressed you will go to the status page, here text information is presented to show the progress of the process.

If a problem occurs it will be reported here.

Finish

Once the files have been processed, new *.mzXML files are created and the Reorder Scans application may start, you can also start Reorder Scans by clisking on the Reorder Scans button in the start screen