The X! search engine project

X! Search Engine Development

  X! HUNTER Annotated Spectrum Library (ASL) pattern matching

A new GPM application, X! HUNTER, has reached to point where it is ready for public testing. X! Hunter is a different style of peptide identification search engine. Rather than predicting spectra from a peptide sequence, it directly compares an input spectrum to a library of spectra that have been confidently assigned to a particular peptide sequence (an Annotated Spectrum Library, or ASL). This type of pattern matching tool is ideal for applications such as biomarker discovery, molecular scanners and instrument control, where obtaining a confident match for a single spectrum quickly is important.

Using ASLs is not at all new: this type of pattern matching strategy has been used in all forms of analytical spectroscopy (including mass spectrometry) since the 1950's. The only reason it hasn't been applied to peptide mass spectra is the obvious difficulty of obtaining exemplar spectra for all of the possible peptides in a proteome.

Fortunately, we happen to have a database of over two hundered million examples, GPMDB. To create the ASLs for X! Hunter, all of the confident assignments for human and yeast peptides were extracted from GPMDB. Then spectra that were replicate observations of the same peptide were averaged together and a final list of averaged peptide spectra was produced.

Please give X! HUNTER a try (there are several examples). Let us know what you think.

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