spectrum, contrast angle

Syntax

The value of this parameter is an floating point number, in the range 0 - 90.

Notes

1. No error message is generated by an invalid value for this parameter.
2. The default value for this parameter is 0

Description

When spectrum, use contrast angle is set to yes, this parameter is used to set the stringency of filtering used to remove redundant peptide spectra from a list of spectra. The value is applied to the spectrum data set according to the following algorithm.

1. The opening angles between all pairs of spectra in the data set are calculated, by computing the inner product of each pair and then dividing it by the lengths of both vectors:
   v = cos^-1(inner(a,b)/(|a||b|))
2. All spectrum pairs that have parent ion masses within 1000 ppm are tested to see if their opening angle v is less than spectrum ,contrast angle.
3. If this test is true, then the most intense spectrum of the pair is kept and the less intensity spectrum is deleted from the list to be searched.