The MS/MS peak picker is a module for detection of peaks which has a MS/MS (MS2). Its purpose is to look through the whole raw data, looking for MS2 scans and try to make a list of chromatographic peaks which has fragmentation scan (MS2).
First look for each MS2 scan on the selected file, obtains information of his parent scan and if a base peak ion, in the a specific range is found, a simple chromatographic peak is formed. The verification of a base peak ion helps to avoid cases when the fragmentation (MS2) scan is coming from a random event. Each one of the detected peaks contains only one scan, after this detection is possible to use another tool like Peak detection - Peak extender.