X! Tandem, P3 and Hunter are open source proteomics software that attempt to find the best sequence model for a given MS/MS spectrum of a peptide. These X! Series search engines use a common set of input parameters, which include a larger set of input parameters than the older styles of search software. The goal of this project is to create a good set of documentation for all of the parameters currently supported by the X! Series. Currently, more than 40 of the API parameters have documentation.
In addition to the text documentation, there are some Universal Modelling Language (UML) diagrams that illustrate some of the more technical features of how the X! Series works here.
Click on the entries below for a description of the appropriate API parameter. X! Series API parameters are represented as ASCII entries in an input file, that uses a simplified XML syntax. A general entry is as follows:
<note type="input" label="GROUP, NAME">VALUE</note>
Each parameter value is a BIOML <note> tag, with the type attribute "input". The label attribute contains the name of the parameter, broken into two parts by a comma. The first part is a general description of a general group of parameters (GROUP) and the second part is the specific description of the parameter (NAME). The VALUE(contents) of the note tag is the value that the parameter will take. The names and values for parameters are case sensitive.
To see an example of a fully filled out X! Series input API file, click here.
Use of all documentation for X! Tandem, X! P3 and X! Hunter is governed by the Artistic License.
Is there something you would like to see included, or documentation that you would like to contribute? Please let use know - firstname.lastname@example.org.
X! Series API description project