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Instance document examples: SpectraST #18

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Create instance document example for SpectraST

Original issue reported on code.google.com by dcre...@gmail.com on 1 May 2008 at 10:33

GoogleCodeExporter commented 8 years ago 
Fragment of example search database for spectraST

Name: AAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAGHVTQAR/4
MW: 3830.819
Comment: Spec=Consensus Pep=N-Semitryp_insource_confirmed
Fullname=Q.AAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAGHVTQAR.M/4 Mods=0 Parent=957.705 
Inst=it
Mz_diff=0.835 Mz_exact=957.7048 Mz_av=958.263
Protein="IPI00025499.1|SWISS-PROT:P10636-8|REFSEQ_NP:NP_005901|ENSEMBL:ENSP00000
303214
Tax_Id=9606 Microtubule-associated protein tau isoforM 2" Pseq=92 
Organism="human"
Se=1^O2:ex=2.005e-011/2.005e-011,td=372925/3.721e+005,pr=1.1e-015/1.1e-015,bs=4.
11e-299,b2=4.01e-011,bd=850
Sample=1/sigma_proof_of_concept_cam,2,2 Nreps=2/2 Missing=0.0901/0.0119
Parent_med=958.54/0.03 Max2med_orig=136.6/20.3 Dotfull=0.847/0.000
Dot_cons=0.933/0.019 Unassign_all=0.053 Unassigned=0.047 Dotbest=0.95 
Flags=2,1,0
Naa=38 DUScorr=1.9/1.9/0.38 Dottheory=0.78 Pfin=2.7e+009 Probcorr=0.82
Tfratio=9.7e+008 Pfract=0
Num peaks: 120
476.3   117     "? 2/2 1.4"
578.5   154     "b17^3/-0.10,b12-46^2/-0.29 2/2 0.4"
579.6   62      "b12-44^2/-0.19,b12-45^2/0.31 2/2 0.0"
643.4   78      "b13-18^2/0.09,b20-46^3/-0.24 2/2 0.1"
649.6   123     "a7/0.27 2/2 1.4"
673.1   95      "? 2/2 1.0"
686.6   73      "b28-46^4/0.03,b28-45^4/-0.22 2/2 0.1"
694.3   181     "b14-18^2/0.47,b14-17^2/-0.03 2/2 1.1"
703.1   106     "b14^2/0.27 2/2 0.1"
706.3   66      "? 2/2 0.3"
711.8   101     "y6/0.41 2/2 0.2"
729.5   291     "b15-18^2/0.15,b15-17^2/-0.35 2/2 0.3"
738.5   255     "b15^2/0.15 2/2 1.1"
744.1   93      "b23-18^3/0.09,b23-17^3/-0.24 2/2 0.4"
746.8   76      "? 2/2 0.4"
761.7   58      "b31-17^4/0.10,b31-18^4/0.35 2/1 0.2"
768.2   119     "y7/-0.21,y15-45^2/-0.19 2/2 0.6"
788.9   65      "y31^4/0.28,b8-17/-0.47 2/2 0.1"
791.1   1488    "y15^2/0.21 2/2 0.8"
792.2   105     "y15i^2/1.31 2/2 0.5"
794.1   148     "b16-18^2/0.23,b16-17^2/-0.27 2/2 1.1"
796.7   86      "b25-44^3/-0.00,b25-45^3/0.33 2/2 0.6"
797.7   108     "b25-44i^3/1.00 2/2 1.3"
803.3   341     "b16^2/0.43,y24-18^3/0.59 2/2 2.4"
804.3   181     "b16i^2/1.43 2/2 1.8"
806.8   122     "b8/0.43 2/2 0.7"
808.5   69      "y24^3/-0.21 2/2 0.1"
811.0   100     "b25^3/-0.37 2/2 0.4"
825.7   60      "? 2/2 0.0"
832.0   147     "y16-18^2/-0.41 2/2 0.7"
835.6   69      "? 2/2 0.2"
841.8   1719    "y16^2/0.39,y25^3/-0.60 2/2 2.9"
842.6   201     "y25^3/0.20,b26-18^3/-0.47 2/2 1.1"
846.7   96      "? 2/2 0.2"
848.4   98      "y33^4/0.25 2/2 0.0"
849.5   85      "b26^3/0.43 2/2 0.2"
858.7   298     "b17-17^2/-0.20,b17-18^2/0.30 2/2 1.5"
866.1   94      "? 2/2 0.1"
867.7   961     "b17^2/0.30,y34-18^4/-0.21 2/2 6.1"
868.8   204     "b17i^2/1.40 2/2 2.1"
881.6   89      "? 2/2 0.3"
885.1   152     "b36-45^4/-0.06,b36-46^4/0.19 2/2 0.1"
886.6   253     "b27-17^3/0.19,b27-18^3/0.52 2/2 0.5"
888.5   221     "y27-18^3/-0.59 2/2 2.0"
890.1   899     "y17-18^2/0.18,y17-17^2/-0.32 2/2 0.8"
891.1   397     "y17-18i^2/1.18 2/2 2.7"

Original comment by jensie...@gmail.com on 17 Sep 2008 at 3:16

GoogleCodeExporter commented 8 years ago 
Added an example document to the svn.  Just a comment that because there is no
protein determination step there is no relationship defined in the document 
between
DBSequence and peptide in the SequenceCollection - as a result the DBSequences 
never
get referenced.

Original comment by jensie...@gmail.com on 24 Sep 2008 at 1:12

GoogleCodeExporter commented 8 years ago

Original comment by andrewro...@googlemail.com on 16 Oct 2008 at 3:58