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:

1. SEARCH=MIS [required]
2. REPTYPE=Peptide [required]
3. 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]
204.18 22
215.04 3
232.07 27
238.28 3
257.3 3
258.26 4
275.31 9
301.31 3
319.13 7
327.71 5
387.16 3
388.36 7
414.18 10
475.33 100
542.34 5
543.3 8
546.36 8
560.25 12
689.39 4
END IONS				[end of a spectrum]

NOTES:

1. The spectra are not stored in any particular order: spectra associated with the same protein may be located anywhere within the file.
2. Annotations are based on sequence accession numbers for particular sequence collections, e.g., ENSEMBL, IPI or SWISS-PROT protein accession numbers.
3. X! Hunter ASLs store the twenty (20) most intense peaks for a particular MS/MS spectrum.
4. Parent ion masses are calculated based on the mono-isotopic masses of the peptide residues.