spectrum, minimum cosine theta


The value of this parameter is an floating point number, in the range 0 - 1.0.


  1. No error message is generated by an invalid value for this parameter.
  2. The default value for this parameter is 0.3


This parameter is used to set the stringency of filtering used to identify experimental peptide spectra from an annotated spectrum library. 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:
    cos(Θ) = cos-1(inner(a,b)/(|a||b|))
  2. All spectrum pairs that have parent ion masses within the appropriate parent ion mass tolerances are tested to see if their cos(Θ) is greater than spectrum, minimum cosine theta.
  3. If this test is true, then the match is stored, if it is the current best match.

see also: spectrum, parent monoisotopic mass error minus | spectrum, parent monoisotopic mass error plus |

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