I'm trying to work with the peptide spectra provides in the spc library. I open the file with extension .sptxt, and the content is like following
## COMPILE from cons08.splib [QUALITY_FILTER;r=1;q=0.6;L=0;l=5;1=TRUE;i=0.999;e=TRUE] ### > cons08.splib : COMPILE from "raw08.splib" [CONSENSUS;r=1;q=0.6;x=100;w=SN;k=TRUE;d=150;p=300] ### > > raw08.splib : IMPORT from PepXML: "HumanDataInteract.xml" (SEQUEST against "/home/sorcerer/fasta/ ipi.HUMAN.v3.26.fasta" (AA)) [P=0.8;n=TiO2;t=0;v=100000;g=FALSE;u=0] ### === Name: IYQY[243]IQSR/3 LibID: 0 MW: 1152.5438 PrecursorMZ: 384.1813 Status: Normal FullName: R.IYQY[243]IQSR.F/3 Comment: AvePrecursorMz=384.4051 BinaryFileOffset=378 ConsFracAssignedPeaks=0.708 DeltaCn=0.1070 DotConsensus=0.85,0.02;0/2 FracUnassigned=0.00,0/5;0.02,2/20;0.06,19/65 Inst=0 MaxRepSN=47.9 Mods=1/3,Y,Phospho NAA=8 NMC=0 NTT=2 Nreps=2/2 OrigMaxIntensity=4.1e +03 Parent=384.181 Pep=Tryptic Prob=0.9332 ProbRange=0.989579,0.9332,0.8886,0.844 Protein=8/IPI00182717/ IPI00000352/IPI00014344/IPI00215873/IPI00219250/IPI00219251/ IPI00219252/IPI00332215 RepFracAssignedPeaks=0.492 RepNumPeaks=216.5/56.5 RetentionTime=0.0,0.0,0.0 SN=200.0 Sample=1/ TiO2,2,2 Se=1^S2:dc=0.1320/0.0250,fv=2.0476/0.1727,pb=0.8886/0.0446,xc=2.4030/0.0450 Spec=Consensus XCorr=2.4480 NumPeaks: 65 130.1072 30.0 y3^3/-0.63,b3-17^3/0.04 2/2 0.0455|0.42 171.0304 64.7 ? 2/2 0.0313|1.02 174.9999 136.1 y1/-0.12 2/2 0.1313|0.21 186.6766 177.6 y3-18^2/0.07,y3-17^2/-0.42 2/2 0.0176|0.25 191.0824 45.3 b4-80^3/0.99 2/2 0.0093|0.87 195.4363 225.6 y3^2/-0.17,b3-17^2/0.84 2/2 0.0892|0.34 197.0844 30.3 ? 2/2 0.0020|0.99 215.0593 43.7 ? 2/2 0.1230|0.27 215.9981 140.3 b4^3/-0.75,y5-98^3/-0.79,b5-116^3/0.21 2/2 0.0676|0.03 226.8692 14.9 b5-80^3/-0.92 2/2 0.0137|0.43 229.0984 48.5 y4-45^2/-0.54 2/2 0.0240|0.38 231.0454 10.0 ? 2/2 0.0020|0.56 242.1390 87.8 ? 2/2 0.0196|0.72 243.1096 67.1 y4-18^2/-0.04,y5-18^3/-0.33 2/2 0.0289|0.62 243.9398 51.4 y2-18/-0.20,y4-17^2/0.30,y5-17^3/0.17 2/2 0.0034|0.67 245.1060 24.0 y2-17/-0.02,a5^3/-0.01 2/2 0.0539|0.24 262.0760 2395.6 y2/-0.08 2/2 0.0318|0.07 263.1250 189.8 y2i/0.05 2/2 0.0343|0.29 276.6047 35.8 b2/-0.55,y6-45^3/-0.52,b4-98^2/0.97 2/2 0.1259|0.48 280.2172 31.6 ? 2/2 0.0353|0.08 290.1435 53.4 ? 2/2 0.0754|0.30 309.1732 47.5 ? 2/2 0.0622|0.82 324.3744 215.8 b4^2/-0.25,y5-98^2/-0.30 2/2 0.0411|0.01 325.0726 105.5 b4^2i/0.20 2/2 0.0632|0.22 329.0662 55.3 ? 2/2 0.0113|0.11 340.1576 98.1 p-134^3/0.64,y7-17^3/-0.65,y7-18^3/-0.33 2/2 0.0519|0.56 341.1334 25.8 b5-80^2/-0.05 2/2 0.0142|0.28 342.8666 916.5 ? 2/2 0.0029|0.95 355.0901 96.0 ? 2/2 0.1166|0.20 356.0571 115.0 ? 2/2 0.0970|0.38 360.1717 110.6 b3-45/-0.02 2/2 0.0916|0.95 361.0927 34.7 b3-45i/-0.08 2/2 0.0862|0.64 362.9919 43.1 ? 2/2 0.0847|0.00 364.9947 213.8 y5-18^2/0.33,y5-17^2/-0.16 2/2 0.1969|0.25 367.0821 10000.0 a5^2/-0.09 2/2 0.0735|0.00 368.4888 205.7 ? 2/2 0.0309|0.17 369.4100 73.9 p-45^3/0.24 2/2 0.0049|0.17 372.2138 1906.3 y3-18/0.01,p-36^3/0.03,p-35^3/-0.30,b5-17^2/-0.44 2/2 0.0647|0.01 373.1972 1194.2 y5^2/-0.47,y3-17/0.01,p-34^3/0.35 2/2 0.0602|0.32 374.2436 242.0 y3-17i/0.05 2/2 0.0387|0.01 375.4273 472.5 y3-17i/0.23 2/2 0.2013|0.25 378.1030 702.5 p-18^3/-0.07,p-17^3/-0.40,a3/0.88 2/2 0.0539|0.20 378.9725 64.3 y6-116^2/-0.73 2/2 0.0901|0.02 384.8119 391.4 p^3/0.63 2/2 0.0759|0.16 390.0674 7462.9 y3/-0.14 2/2 0.0201|0.06 391.0985 814.1 y3i/0.03 2/2 0.0950|0.18 402.8832 26.0 ? 2/2 0.0108|0.83 404.9691 301.2 b3/-0.24,b6-80^2/-0.24 2/2 0.1141|0.04 428.8291 257.8 y6-18^2/0.14,y6-17^2/-0.35 2/2 0.1239|0.36 437.5736 191.5 y6^2/-0.12,b6-17^2/0.89 2/2 0.0632|0.48 438.3828 48.7 ? 2/2 0.0480|0.05 444.9526 1408.1 b6^2/-0.24 2/2 0.0103|0.16 445.6008 383.6 b6^2i/0.15 2/2 0.0113|0.15 447.4074 50.9 ? 2/2 0.0103|0.25 484.9427 100.0 y4-18/-0.34 2/2 0.0617|0.42 486.2818 40.7 y4-17/0.01 2/2 0.0426|0.65 488.7415 148.0 b7^2/0.03 2/2 0.0730|0.01 503.1456 99.5 y4/-0.15 2/2 0.0607|0.10 525.0845 59.0 ? 2/2 0.0754|0.07 536.2040 82.7 ? 2/2 0.0661|0.31 647.9426 3016.5 b4/-0.30,y5-98/-0.40 2/2 0.0000|0.20 648.9694 990.9 b4i/0.03 2/2 0.0397|0.10 743.7762 25.7 b5-17/-0.52 2/2 0.0598|0.06 761.0124 546.3 b5/-0.31 2/2 0.0167|0.21 761.9772 62.8 b5i/-0.04 2/2 0.0309|0.35 Could any one help me on interpretation of the content. I guess the first column for data part is m/z value and the second column is intensity (maybe in ion count). But I have no idea with the rest part. Basically, what I want to do is to recover the experimental spectra for peptides from the library. Thank you very much --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
