The X! Hunter Annotated Spectrum Library (ASL) system normally uses a binary
file format to record the spectra and annotation. This format is a beta-test
format that will allow the use of text formatted files, using a simple
extension of the Mascot Generic File format.
The file has a small header section with three entries:
- SEARCH=MIS [required]
- REPTYPE=Peptide [required]
- LIBSIZE=nnn [required, where nnn = number of spectra in the file]
The annotation and spectra
are stored sequentially. Each spectrum in the library begins with BEGIN IONS and
ends with END IONS. A typical entry is as follows:
BEGIN IONS [start of a spectrum]
PEPMASS=353.681 [parent ion m/z value]
CHARGE=2 [parent ion charge]
PEPSEQ=CASLQK [peptide sequence]
PEPEXP=1.22866e-007 [annotation confidence]
PEPMOD=57.0215@1 [peptide modification and position]
PEPACC=sp|ALBU_BOVIN|@223 [protein accession number and position]
PEPACC=sp|ALBU_HUMAN|@224 [protein accession number and position]
GPMp=GPMp0504028113 [peptide accession number]
187.15 3 [ion m/z and intensity]
END IONS [end of a spectrum]
- The spectra are not stored in any particular order: spectra associated with the
same protein may be located anywhere within the file.
- Annotations are based on sequence accession numbers for particular sequence collections,
e.g., ENSEMBL, IPI or SWISS-PROT protein accession numbers.
- X! Hunter ASLs store the twenty (20) most intense peaks for a particular MS/MS spectrum.
- Parent ion masses are calculated based on the mono-isotopic masses of the peptide residues.