protein, use annotations

# protein, use annotations ## Syntax This parameter is a text string that may be yes or no. ## Notes Introduced in version 2008.02.01. Default value is no The value of this parameter is only used in the first round of identification: to apply the annotations to refinement rounds, use the refine, use annotations parameter. ## Description It is known that different proteins have different post-translational modifications. In some cases, proteins may be highly modified by unusual modifications, such as the highly variable modification of histones or collagens. When the parameter is set to yes, an annotation file that contains the modifications known to be present in each protein will be added to the search, on a protein by protein basis. Any other modifications that you have specified will over-ride these annotations, if there is a conflict between the annotation and your specified modification. see also: refine, use annotations | X! TANDEM API description project