spectrum, neutral loss window

# spectrum, neutral loss window ## Syntax This value is a positive floating point number, Wnl > 0. ## Notes No error message is generated when an uninterpretable value is entered for this parameter. The value of this parameter is ignored if spectrum, use neutral loss window = yes ## Description Some types of post-translational or chemical modifications can produce intense peaks in a spectrum because of a favoured fragmentation mechanism produced by the loss of a stable neutral molecule. These "neutral loss" peaks can be removed from a spectrum by setting appropriate values for the Wnl and spectrum, neutral loss mass, Mnl parameters. If the spectrum, use neutral loss window value is yes, then any peaks with an m/z value that meets the following condition is rejected: | m/z - Mnl | < Wnl Any peak that has been removed using this mechanism is reinserted into the spectrum before the spectrum is written to the output XML data file, even though it was not considered during the peptide modelling process. see also: spectrum, neutral loss mass | spectrum, use neutral loss window X! TANDEM API description project