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  X! HUNTER ASL statistics, v. 2010.08.15

The current build of the X! Hunter ASLs is 2010.08.15.

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) were excluded from this build. Heavy SILAC labelled peptides are separated into their own libraries, when the number of peptides observed is sufficient to create a useful library. 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
A. carolinensis [Anole lizard] 249,578 55,469 ×4.5
A. fumigatus 14,422 7,990 ×1.8
A. mellifera [bee] 38,452 18,964 ×2.0
A. thaliana 111,689 62,574 ×1.8
B. taurus [cow] 592,070 140,063 ×4.2
B. taurus (silac) 82,009 35,609 ×2.3
C. elegans 190,952 90,981 ×2.1
C. familiaris [dog] 401,953 101,332 ×4.0
C. familiaris (silac) 84,549 36,932 ×2.3
cRAP 76,845 17,078 ×4.5
cRAP (silac) 2,639 737 ×3.6
C. porcellus [Guinea pig] 547,205 126,992 ×4.3
C. porcellus (silac) 77,889 33,661 ×2.3
D. melanogaster 122,353 71,928 ×1.7
D. rerio [zebrafish] 174,049 46,546 ×3.7
D. rerio (silac) 24,726 10,107 ×2.4
F. cattus [cat] 404,073 95,431 ×4.2
F. cattus (silac) 58,473 25,011 ×2.3
G. gallus [chicken] 265,844 68,927 ×3.9
G. gallus (silac) 41,965 17,370 ×2.4
E. caballus [horse] 590,514 139,849 ×4.2
E. caballus (silac) 83,448 36,595 ×2.3
H. sapiens [human] 1,002,326 270,345 ×3.7
H. sapiens (silac) 127,406 60,617 ×2.1
M. mulata [Macaque] 754,601 195,701 ×3.9
M. mulatta (silac) 105,274 48,286 ×2.2
M. musculus [mouse] 732,382 199,182 ×3.7
M. musculus (silac) 94,198 41,684 ×2.3
O. cuniculus [rabbit] 392,132 89,916 ×4.4
O. cuniculus (silac) 55,216 23,860 ×2.3
P. troglodytes [chimpanzee] 889,232 238,688 ×3.7
P. troglodytes (silac) 117,759 55,572 ×2.1
R. norvegicus [rat] 637,776 160,439 ×4.0
R. norvegicus (silac) 82,859 36,026 ×2.3
S. cerevisiae [yeast] 201,253 133,166 ×1.5
S. cerevisiae (silac) 65,001 42,907 ×1.5
S. scrofa [pig] 442,151 105,386 ×4.2
S. scrofa (silac) 65,245 27,892 ×2.3
S. pombe 9,960 5,456 ×1.8
T. rubripes [fugu] 169,551 36,514 ×4.6
T. rubripes (silac) 23,512 9,748 ×2.4
X. tropicalis [Western clawed frog] 202,040 43,386 ×4.7
X. laevis [Common Platanna] 205,149 42,208 ×4.9

Prokaryote libraries:

File   Spectra Peptides Redundancy
Bacillus anthracis A0248 31,483 17,463 ×1.8
Bacillus anthracis Ames 0581 31,601 17,525 ×1.8
Bacillus anthracis Ames 30,896 17,054 ×1.8
Bacillus anthracis CDC 684 31,599 17,534 ×1.8
Bacillus anthracis str Sterne 30,967 17,097 ×1.8
Brucella abortus bv 1 9 941 4,441 1,715 ×2.6
Brucella abortus S19 4,503 1,730 ×2.6
Brucella melitensis ATCC 23457 4,460 1,720 ×2.6
Brucella melitensis biovar Abortus 4,486 1,727 ×2.6
Brucella melitensis 4,520 1,733 ×2.6
Brucella ovis 4,403 1,636 ×2.7
Brucella suis 1330 4,484 1,718 ×2.6
Brucella suis ATCC 23445 4,519 1,719 ×2.6
Campylobacter jejuni 81-176 3,373 2,060 ×1.6
Campylobacter jejuni 81116 3,256 1,932 ×1.7
Campylobacter jejuni 3,236 1,928 ×1.7
Campylobacter jejuni doylei 269 97 2,891 1,626 ×1.8
Campylobacter jejuni RM1221 3,218 1,896 ×1.7
Clostridium botulinum A 2,989 1,129 ×2.6
Clostridium thermocellum ATCC 27405 6,209 3,911 ×1.6
Deinococcus radiodurans 16,454 10,313 ×1.6
Escherichia coli 0127 H6 E2348 69 171,362 42,267 ×4.1
Escherichia coli 536 169,987 41,956 ×4.1
Escherichia coli 55989 174,855 43,453 ×4.0
Escherichia coli APEC O1 163,670 40,971 ×4.0
Escherichia coli BL21 DE3 173,972 43,207 ×4.0
Escherichia coli BW2952 175,975 43,832 ×4.0
Escherichia coli B REL606 174,429 43,316 ×4.0
Escherichia coli CFT073 167,801 41,587 ×4.0
Escherichia coli C ATCC 8739 174,977 43,515 ×4.0
Escherichia coli E24377A 174,568 43,344 ×4.0
Escherichia coli ED1a 169,957 41,948 ×4.1
Escherichia coli HS 173,693 43,150 ×4.0
Escherichia coli IAI1 174,758 43,395 ×4.0
Escherichia coli IAI39 171,448 42,449 ×4.0
Escherichia coli K 12 substr DH10B 170,426 42,246 ×4.0
Escherichia coli K 12 substr MG1655 176,715 44,136 ×4.0
Escherichia coli K 12 substr W3110 176,683 44,128 ×4.0
Escherichia coli O103 H2 12009 175,554 43,659 ×4.0
Escherichia coli O111 H 11128 173,684 43,305 ×4.0
Escherichia coli O157H7 177,474 44,594 ×4.0
Escherichia coli O157H7 EDL933 176,355 44,380 ×4.0
Escherichia coli O157 H7 EC4115 176,655 44,302 ×4.0
Escherichia coli O157 H7 TW14359 177,324 44,505 ×4.0
Escherichia coli O26 H11 11368 175,137 43,709 ×4.0
Escherichia coli O55 H7 CB9615 uid46655 176,007 44,073 ×4.0
Escherichia coli S88 172,044 42,579 ×4.0
Escherichia coli SE11 175,728 43,655 ×4.0
Escherichia coli SMS 3 5 173,263 43,038 ×4.0
Escherichia coli UMN026 174,296 43,375 ×4.0
Escherichia coli UTI89 172,043 42,589 ×4.0
Francisella tularensis tularensis 11,025 4,683 ×2.4
Halobacterium salinarum R1 2,350 1,702 ×1.4
Halobacterium sp 2,350 1,704 ×1.4
Leptospira interrogans serovar Copenhageni 22,971 14,752 ×1.6
Leptospira interrogans serovar Lai 22,435 14,368 ×1.6
Mycobacterium smegmatis MC2 155 16,130 8,611 ×1.9
Mycobacterium tuberculosis CDC1551 32,846 18,623 ×1.8
Mycobacterium tuberculosis F11 33,321 18,905 ×1.8
Mycobacterium tuberculosis H37Ra 33,404 18,951 ×1.8
Mycobacterium tuberculosis H37Rv 33,372 18,934 ×1.8
Mycobacterium tuberculosis KZN 1435 33,336 18,919 ×1.8
Salmonella enterica arizonae serovar 62 z4 z23 170,967 43,098 ×4.0
Salmonella enterica Choleraesuis 200,596 53,037 ×3.8
Salmonella enterica Paratypi ATCC 9150 201,913 53,156 ×3.8
Salmonella enterica serovar Agona SL483 202,988 53,634 ×3.8
Salmonella enterica serovar Dublin CT 02021853 201,877 53,603 ×3.8
Salmonella enterica serovar Enteritidis P125109 207,364 55,062 ×3.8
Salmonella enterica serovar Gallinarum 287 91 199,192 52,370 ×3.8
Salmonella enterica serovar Heidelberg SL476 205,298 54,747 ×3.7
Salmonella enterica serovar Newport SL254 204,464 54,302 ×3.8
Salmonella enterica serovar Paratyphi A AKU 12601 201,510 53,064 ×3.8
Salmonella enterica serovar Paratyphi B SPB7 205,674 54,749 ×3.8
Salmonella enterica serovar Paratyphi C RKS4594 202,251 53,626 ×3.8
Salmonella enterica serovar Schwarzengrund CVM19633 201,863 53,376 ×3.8
Salmonella enterica serovar Typhi Ty2 208,886 55,195 ×3.8
Salmonella typhimurium LT2 213,194 57,608 ×3.7
Salmonella typhi 208,127 54,993 ×3.8
Shewanella oneidensis 29,470 13,953 ×2.1
Shigella dysenteriae 162,151 39,569 ×4.1
Staphylococcus aureus aureus MRSA252 25,240 13,849 ×1.8
Staphylococcus aureus aureus MSSA476 25,884 14,295 ×1.8
Staphylococcus aureus COL 25,888 14,264 ×1.8
Staphylococcus aureus ED98 26,213 14,568 ×1.8
Staphylococcus aureus JH1 26,929 14,926 ×1.8
Staphylococcus aureus JH9 26,909 14,905 ×1.8
Staphylococcus aureus Mu3 26,860 14,886 ×1.8
Staphylococcus aureus Mu50 26,867 14,886 ×1.8
Staphylococcus aureus MW2 25,964 14,329 ×1.8
Staphylococcus aureus N315 26,859 14,868 ×1.8
Staphylococcus aureus NCTC 8325 25,653 14,210 ×1.8
Staphylococcus aureus Newman 25,858 14,289 ×1.8
Staphylococcus aureus RF122 24,324 13,410 ×1.8
Staphylococcus aureus USA300 FPR3757 26,014 14,385 ×1.8
Staphylococcus aureus USA300 TCH1516 24,640 13,610 ×1.8
Streptococcus pyogenes M1 GAS 11,508 6,060 ×1.9
Streptococcus pyogenes Manfredo 10,951 5,737 ×1.9
Streptococcus pyogenes MGAS10270 11,035 5,822 ×1.9
Streptococcus pyogenes MGAS10394 10,954 5,747 ×1.9
Streptococcus pyogenes MGAS10750 11,029 5,803 ×1.9
Streptococcus pyogenes MGAS2096 10,957 5,752 ×1.9
Streptococcus pyogenes MGAS315 10,972 5,793 ×1.9
Streptococcus pyogenes MGAS5005 11,613 6,127 ×1.9
Streptococcus pyogenes MGAS6180 11,080 5,845 ×1.9
Streptococcus pyogenes MGAS8232 10,909 5,728 ×1.9
Streptococcus pyogenes MGAS9429 11,032 5,796 ×1.9
Streptococcus pyogenes NZ131 10,790 5,687 ×1.9
Streptococcus pyogenes SSI-1 10,855 5,733 ×1.9
Yersinia pestis Angola 54,682 15,051 ×3.6
Yersinia pestis Antiqua 56,597 15,809 ×3.6
Yersinia pestis biovar Microtus 91001 56,481 15,677 ×3.6
Yersinia pestis CO92 56,062 15,629 ×3.6
Yersinia pestis KIM 10 uid288 56,217 15,675 ×3.6
Yersinia pestis Nepal516 56,589 15,735 ×3.6
Yersinia pestis Pestoides F 56,496 15,727 ×3.6
Yersinia pestis Z176003 uid47317 54,445 15,227 ×3.6

Virus libraries:

File   Spectra Peptides Redundancy
Human immunodeficiency virus 1 8 7 ×1.1
Influenza A virus A Puerto Rico 8 34 H1N1 522 342 ×1.5
Monkeypox virus Zaire 96 I 16 3,824 2,031 ×1.9
Respiratory syncytial virus 164 129 ×1.3
Saccharomyces cerevisiae virus L A L1 1,013 662 ×1.5
Saccharomyces cerevisiae virus L BC La 162 107 ×1.5
Vaccinia virus 3,737 1,974 ×1.9
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