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X! HUNTER ASL statistics, v. 2009.05.01

The current build of the X! Hunter ASLs is 2009.05.01.

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 corresponding protein sequence data can be obtained from /projects/xhunter/fasta. The ASL information is recorded in three different formats, depending on how it will be used:

  1. the individual peptide sequences for the major ASL species are given in FASTA format (peptide);
  2. the annotated spectra in Mascot Generic Format, suitable for bioinformatics investigations (MGF); and
  3. the annotated spectra in HLF format, suitable for direct use with X! Hunter (HLF).

Eukaryote libraries:

File    Spectra Peptides Redundancy
afumigatus_cmp_20 13,369 6,886 ×1.9
ath1_cmp_20 69,823 44,123 ×1.6
ath1_ipi_cmp_20 69,831 44,117 ×1.6
cat_cmp_20 275,586 65,804 ×4.2
cavia_cmp_20 368,068 87,107 ×4.2
chicken_cmp_20 204,652 50,218 ×4.1
chimp_cmp_20 592,351 161,286 ×3.7
cow_cmp_20 393,884 95,697 ×4.1
cow_ipi_cmp_20 358,151 89,659 ×4.0
crap_cmp_20 38,499 9,305 ×4.1
dog_cmp_20 404,912 96,750 ×4.2
fish_cmp_20 124,368 36,201 ×3.4
horse_cmp_20 396,454 95,619 ×4.1
human_cmp_20 665,664 181,789 ×3.7
human_ipi_cmp_20 593,442 167,023 ×3.6
human_silac_20 72,729 40,622 ×1.8
mouse_cmp_20 496,873 139,668 ×3.6
mouse_ipi_cmp_20 442,148 127,591 ×3.5
mouse_silac_20 44,052 23,038 ×1.9
rabbit_cmp_20 264,545 61,677 ×4.3
rat_cmp_20 419,442 107,034 ×3.9
rat_ipi_cmp_20 389,057 103,202 ×3.8
spombe_cmp_20 8,885 2,647 ×3.4
worm_cmp_20 99,299 50,822 ×2.0
yeast_cmp_20 151,162 71,255 ×2.1
yeast_silac_20 58,681 40,671 ×1.4

Prokaryote libraries:

File   Spectra Peptides Redundancy
b_anthracis_cmp_20 21,971 13,218 ×1.7
d_radiodurans_cmp_20 11,048 7,571 ×1.5
Escherichia_coli_APEC_O1_cmp_20 65,672 21,603 ×3.0
Escherichia_coli_C_ATCC_8739_cmp_20 69,988 22,915 ×3.1
Escherichia_coli_HS_cmp_20 69,672 22,778 ×3.1
Escherichia_coli_K12_cmp_20 67,936 22,215 ×3.1
Escherichia_coli_O157H7_cmp_20 69,588 22,611 ×3.1
halobacterium_cmp_20 1,435 1,107 ×1.3
m_smegmatis_cmp_20 5,348 3,100 ×1.7
m_tuberculosis_cmp_20 2,374 1,127 ×2.1
s_aureus_cmp_20 2,563 1,361 ×1.9
s_enterica_cmp_20 114,033 37,737 ×3.0
s_oneidensis_cmp_20 17,603 10,119 ×1.7
s_pyogenes_cmp_20 7,630 4,434 ×1.7
s_typhimurium_cmp_20 121,690 41,057 ×3.0
s_typhi_cmp_20 118,332 39,259 ×3.0

Some additional annotation can be obtained from these collections.

Peptides representing N-terminal acetylation of proteins:

  1. Homo sapiens.
  2. Saccharomyces cerevisiae.
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