Tolerance

Tolerance needs to contain the maximum allowed m/z shift of peaks within one spectrum relative to each other. It is in atomic mass units (amu) and must be a floating point number greater than zero. During a search, a theoretical spectrum is iteratively shifted across the search window in increments of “tolerance”. At each shift, each theoretical peak is matched to experimental peaks within its m/z tolerance (if any). Thus, “tolerance” is not sensitive to a systematic m/z bias because it will automatically be subtracted in one of the search windows. It is sensitive to random shifts of individual peaks and should exceed the resolution of the instrument.