Peaks need to be matched across samples in order to be compared. For two-column format (mass and intensities), peaks are grouped by their m/z values. For three column data (mass, retention time, and intensities), the program will further group peaks based on their retention time. Users need to supply tolerance values in order to proceed. Here are some suggested values: mass tolerance - 0.25 (m/z); retention time - 30 (seconds) for LC-MS peak, and 5 (seconds) for GC-MS peaks. Please note, If a sample has more than one peak in a group, they will be replaced by their sum; some groups will be excluded if none of the classes has at least half its samples represented. Finally, the program create a peak intensity table in which each sample occupies a row and each column represents a peak group identified by the median values of its position (m/z and/or retention time).
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