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. Parent ion mass: m+h m/z , z = 1 2 3 ?
   The parent ion mass is used to limit the number of library spectra compared to the observed spectrum. You may enter either the parent ion mass-to-charge ratio (m/z) or it's assumed mass + 1 proton (m+h). The charge state of the parent ion (z) must also be specified: if it is unknown, selecting z = ? will test z = 1,2 & 3.
2. Mass-intensity pairs:
   155.077 21 169.111 14 173.099 24 175.128 66 187.092 28 203.113 28 213.11 28 215.118 66 231.154 24 259.067 21 270.122 24 274.173 21 284.144 17 286.131 52 288.109 28 331.227 100 341.213 24 359.177 17 360.166 28 369.221 34 387.214 45 399.198 45 417.188 24 431.25 14 453.246 17 480.213 14 494.31 38 516.188 17 622.38 38 750.463 41 821.491 59 934.407 17 935.402 17 1049.61 17 1050.57 21 1137.53 31 1266.62 28 1304.65 3 1316.98 3 1395.78 17 1496.94 17
   
   Enter fragment m/z and intensity pairs, one pair per line.
3. Taxon:
   H. sapiens M. musculus A. thaliana S. cerevisiae
   
   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 the current spectrum libraries by default.
4. Parent mass error: +  -  Daltons
   
   Library spectra with parent ion masses outside of this range will not be matched to observed spectra.
5. Parent ion isotope error: yes no
   
   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 1x13-C or 2x13-C peaks instead.
6. cos(θ) >:
   
   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.
7. log(e) <: 0 -1 -2 -3 -4 -5 -6 -7 -8 -9
   
   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 matches where the likelyhood that the match is 0.01 or less will be reported.
8. Perform search:

Examples: 1 | 2 | 3 | 4

The spectrum file version may be more appropriate for many uses.