X! Hunter is a search engine that compares experimentally observed spectra directly with consensus mass spectra obtained from the GPMDB. It can identify proteins for human, budding yeast, mouse and thale cress samples. Because the sequence modifications and cleavage sites for the peptides in the sequence library are already known, it is not necessary to specify as many parameters for this type of search as in more conventional search engines.

1. Spectra:
   
   parameter name = "spectrum, path" (more ...)
   
   DTA, PKL, MGF, mzData, mzXML or Tandem BIOML format files only
   Files may be compressed in either ZIP or GZIP formats.
2. Taxon:
   

   ENSEMBL:

   Others:

   
   
   parameter name = "protein, taxon" (more ...)
   
   This selection determines which organism was the source of your proteins. As the GPMDB collection grows, other species will be made available. Some common experimental contaminants, such as bovine serum albumin and trypsin are included in each of the current spectrum libraries by default.
   Select one or more species to perform your search.
3. Parent mass error: +  -  Da or ppm
   
   parameter name = "spectrum, parent monoisotopic mass error minus" (more ...)
   parameter name = "spectrum, parent monoisotopic mass error plus" (more ...)
   parameter name = "spectrum, parent monoisotopic mass error units" (more ...)
   
   Library spectra with parent ion masses outside of this range will not be matched to observed spectra.
4. Parent ion isotope error: yes no
   
   parameter name = "spectrum, parent monoisotopic mass isotope error" (more ...)
   
   If this parameter is set to "yes", X! Hunter will assume that it is possible that the parent ion peak picking software may have made a mistake selecting the all 12-C peak from the first MS scan, occasionally selecting the peak corresponding to one or two 13-C atoms instead.
5. cos(θ) >:
   
   parameter name = "spectrum, minimum cosine theta" (more ...)
   
   This parameter sets how closely an observed spectrum matches a library spectrum. Values can be between 0 and 1, where 0 is no match at all and 1 is a perfect match.
   NOTE: if this value is set to 0, a default value will be used instead.
6. Check all charges: yes
   
   parameter name = "spectrum, check all charges"
   
   If this parameter is no, X! Hunter uses the parent charge recorded in a spectrum file. If this parameter is yes, parent ion charges z = 1, 2 or 3 are tested.
7. log(e) <: 0 -1 -2 -3 -4 -5 -6 -7 -8 -9
   
   parameter name = "output, maximum valid expectation value" (more ...)
   
   This parameter sets the maximum value for the expectation value that a particular match between a spectrum and a library spectrum is random.
   For instance, a value of "-2" here means that only assignments where the likelyhood that the match is random is <0.01 will be reported.
8. Perform search:

The single spectrum service may be more appropriate for some uses.