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:

   Alternates: or prokaryotes

   
   
   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. peptide log(e) < 0 -1 -2 -3 -4 -5 -6 -7 -8 -9 and protein 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. peptide sequences:
   
   parameter name = "protein, allowed peptides"
   
   This parameter can be used to enter one or more peptide sequences, separated by commas. When sequences are entered, X! Hunter will only search for those peptide sequences, ignoring all other entries in the annotation libraries. The peptide sequences must be represented as continuous strings of uppercase characters. The following are examples of valid entries for this parameter:
   

     VLIPDETVK
     LIPDEFHR,YGFTQQQQQR,LIVMK
   			

9. protein accessions:
   
   parameter name = "protein, allowed peptides"
   
   This parameter can be used to enter one or more protein accession numbers, separated by commas. When accession numbers are entered, X! Hunter will only search for peptides from the proteins with those accession numbers, ignoring all other entries in the annotation libraries. The accession numbers must be represented in exactly the same way that they are shown in X! Hunter output displays. The following are examples of valid entries for this parameter:
   

     ENSP00000249364
     YLR347C,YLR335W,YGL244W
   			

10. Perform search:

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