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The current build of the X! Hunter ASLs
is 2008.10.01. The expectation values allowed for this build were e < 0.001, i.e.
less than 1 chance in 1000 of being a random assignment.
The spectrum libraries were annotated with the protein
sequence files currently used by the rest of the GPM system. Unmodified
peptides correspond to any peptide sequence that was observed with
the correct parent ion mass corresponding to the theoretical mass
for that peptide sequence. The majoritiy of peptide modifications are composed of
oxidized methionine residues, fixed modifications on cysteine
residues, acetylation and carbamylation modifications of the N-terminus of the peptide, acetylation at lysine residues,
phosphorylation at serine, threonine and tyrosine residues and deamidation of glutamine and asparagine residues. Modifications associated
with specific quantitation reagents (such as ICAT or ITRAC) and any SILAC heavy peptides were excluded from this build.
Both tryptic and non-tryptic peptides were included in this build.
The build process has been altered to re-align any m/z errors in fragment ion peaks to be the exact
m/z associated with the best-fit y- or b-ions (including ammonia and water neutral losses). The build
process also now requires that at least 40% of the peaks in a spectrum (corresponding to at least 40% of the
ion intensity) must be assignable as y- or b-ions or their corresponding neutral losses.
These ASLs can be obtained from the GPM ftp site: /projects/xhunter/libs.
The proteome sequence files can be found at the same site: /projects/xhunter/fasta.
The individual peptide sequences for the major ASL species are given in FASTA format in GPMp.
The spectra corresponding to these peptides are also supplied in Mascot Generic Format in the MGF
directory. These files contain all of the spectra and sequence modification annotation information that is present
in the corresponding HLF file.
| Species |
Proteome |
Unmodified |
Modified |
Total peptides |
| A. thaliana |
ATH1, Tair 6 |
49,737 |
27,659 |
77,396 |
| B. taurus |
BTAU 4.0 | ,
142,015 |
100,494 |
242,509 |
| C. familiaris |
CanFam 2.0 |
145,073 |
102,977 |
248,050 |
| C. porcellus |
cavPor2 |
83,506 |
60,123 |
143,629 |
| D. rerio |
WTSI Zv7 |
40,391 |
30,787 |
71,178 |
| E. caballus |
Equ Cab 2.0 |
142,359 |
100,060 |
242,419 |
| F. catus |
BROAD CAT |
96,914 |
72,982 |
169,896 |
| G. gallus |
WASHUC2 |
79,896 |
59,836 |
139,732 |
| H. sapiens |
NCBI 36 |
228,705 |
189,151 |
417,856 |
| M. musculus |
NCBI m37 |
181,722 |
130,057 |
311,779 |
| O. cuniculus |
RABBIT |
96,351 |
68,388 |
164,739 |
| P. troglodytes |
CHIMP 2.1 |
206,442 |
159,676 |
366,118 |
| R. norvegicus |
RGSC 3.4 |
152,877 |
108,599 |
261,476 |
| S. cerevisiae |
SGD |
42,003 |
22,747 |
64,750 |
| T. rubripes |
FUGU 4.0 |
36,674 |
32,492 |
69,166 |
| cRAP |
GPM |
4,044 |
6,197 |
10,241 |
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Some additional annotation can be obtained from these collections.
Peptides representing N-terminal acetylation of proteins:
- Homo sapiens.
- Saccharomyces cerevisiae.
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