Hi Delphine, Perhaps you can run msconvert using the titleMaker filter to get the appropriate titles? http://proteowizard.sourceforge.net/tools/filters.html Hope this helps, --Luis
On Mon, Mar 17, 2014 at 10:19 AM, Delphine <[email protected]> wrote: > Hello, > > My problem is that in the pepxml files I obtained I get the date of > creation instead of the spectrum name in the spectrum query base name: > > <spectrum_query > spectrum="Mon_Mar_17_17-51-03_2014.spectrum1.17826.17826.2" > start_scan="17826" end_scan="17826" precursor_neutral_mass="798.3666" > assumed_charge="2" index="1"> > <search_result> > > I know where the problem comes from but I don't know how to solve it: I > use the MSconvert tool to create mgf files directly from mzxml; and not > anymore the mzxml convert tool of TPP (when I use this tool to create mgf > files I haven't the problem but the precision of the data is not as good). > Here is an example of a .dat file obtained with "MSconvert mgf files": > > > title=300_19_01_F1P1NS_130402_01%2e12909%2e12909%2e2%20File%3a%22300_19_01_F1P1NS_130402_01%2eraw%22%2c%20NativeID%3a%22controllerType%3d0%20controllerNumber%3d1%20scan%3d12909%22 > rtinseconds=3500.7685 > charge=2+ > mass_min=120.152557 > mass_max=854.517334 > int_min=12.27 > int_max=8.112e+004 > num_vals=556 > num_used1=-1 > > Ions1=147.060516:1004,301.073303:2.819e+004,417.668854:6.303e+004,438.199951:8217,551.288635:8.112e+004,705.313599:1484,747.364929:6927,829.569946:83.96,159.070831:482.7,273.099274:1.938e+004,408.905548:1.821e+004,490.254059:3563,552.289490:1.095e+004,688.307800:1441,737.435181:1725,830.955078:76.48,187.130615:398.4,283.058990:5814,419.373077:1.816e+004,501.401611:3079,602.406799:1634,660.351685:1404,748.384216:1375,822.602905:49.28,204.121643:391.9,284.065918:4531,414.033173:8747,420.332550:2997,542.260010:1502,706.355957:648.1,755.360168:598.1,824.582581:47.64,129.110458:378.3,310.112091:3875,416.542755:7054,470.098206:2247,525.203430:995.9,704.374573:600.9,738.373230:476.7,846.732605:37.75,130.058182:346.1,302.127899:2214,369.180420:6360,502.313385:2003,526.391541:878.8,674.351990:507.8,756.459228:472,828.523193:29.62,142.098785:289.3,274.157837:1387,388.276184:4949,470.703339:1606,557.327332:749.2,625.330566:487.5,754.437073:380.2,832.328918:26.58,199.148651:263.9,309.180420:1217,409.798584:4049,434.531860:1555,523.993042:668.2,687.400085:483.1,787.501343:255.1,837.448669:19.09,176.064224:259.6,256.079529:1111,378.305969:3218,435.294067:1300,565.378052:659.6,623.275391:459.2,769.420044:224,213.119476:196.2,317.218567:838,415.060944:2822,439.273163:1135,603.403870:620.9,661.318115:411.5,722.383850:222.7,120.152557:35.84,123.091377:16.8,126.068588:23.09,128.375442:99.27,130.965729:19.74,132.107086:156.4,133.045166:29.45,136.070572:149.8,139.265701:37.39,139.949966:22.22,141.025009:24.65,148.172012:49.58,152.042587:28.01,156.177948:65.88,157.037277:59.4,160.087997:64.01,161.158615:20.75,166.960129:24.56,169.147583:193.4,170.087082:34.01,171.108978:173.3,172.190247:32.02,173.135681:41.12,174.198731:67.85,175.163742:172.3,177.061462:113.6,181.081940:41.66,182.180725:119,183.071228:109.1,184.112763:66.45,185.326813:52.28,186.366974:164.9,188.205383:107.5,188.950531:77.15,190.081116:16.6,191.147522:18.14,193.166565:33.27,194.593658:134,195.289093:152.9,197.165710:117.3,198.212769:65.84,200.136139:46.7,201.181488:153.5,202.123566:71.62,205.071121:43.55,206.216492:46.92,206.932343:52.51,209.111908:43.8,210.078293:44.62,211.113937:183.5,212.148148:109.9,214.182663:83.6,215.132599:121.2,216.062134:36.41,217.197144:37.25,218.071350:51.31,221.202713:414.8,222.121063:108.2,223.143372:123.7,224.481964:81.42,225.139893:112.9,226.158463:152.8,227.142822:481.8,228.227814:101.4,229.064148:21.38,230.114883:205.4,231.102707:111.8,232.264313:150.6,233.197876:98.47,234.088135:44.56,235.181457:63.47,235.995514:15.09,237.197876:37.79,238.123810:131.4,239.151642:85.23,240.192444:181,241.237610:67.5,242.161499:297.1,243.084076:89.38,244.074646:168.2,245.589325:463.5,246.253723:358.3,247.215576:68.53,248.200256:757.2,249.131683:577.6,250.405762:155.7,251.112152:327.6,251.872498:382.9,253.332550:24,254.163055:111.6,257.090302:49.33,258.207398:201.1,259.134430:41.5,260.191528:185,261.145172:399.1,262.163300:262.8,263.262756:115.7,264.115692:46.26,265.068726:95.55,266.112213:254.2,267.106659:373.8,268.170319:180.7,269.141022:83.93,270.159149:252.4,275.201935:114.7,276.216644:528.6,277.225891:268.4,278.183624:30.72,279.628845:224.1,280.235840:176.4,281.193329:60.13,285.056030:483.3,286.062988:329.2,287.238251:194.8,288.120361:104.5,289.182465:23.64,291.208191:48.33,292.162933:380.5,293.173859:190.7,294.143555:313.4,295.439453:308.2,296.180908:96.93,297.330109:91.29,298.112579:72.25,299.411713:112,303.266785:145.4,304.545502:151.9,305.445953:46.69,306.570831:162.7,307.330994:67.5,308.261566:40.67,311.251404:788.9,312.387543:203.8,313.353302:245.4,314.105530:80.11,315.535675:130.4,316.430328:119.7,318.182800:598.5,319.314972:108.1,320.267364:345.8,321.683899:871.3,322.993378:248.7,324.238648:78.31,325.151306:174.6,326.290772:259.6,327.180695:160.9,328.216034:252.1,329.191620:165.9,330.090851:45.47,331.001709:162.9,331.967194:142.7,333.531555:160.1,335.346985:353,338.307983:629.9,339.206787:281.9,340.152985:222.1,341.858002:244,342.976807:364.9,344.255158:1877,345.210602:349.2,346.522369:96.03,347.171753:98.54,348.210541:143.1,349.103455:16.09,350.123383:148.6,350.802551:175.7,352.287659:501.4,353.165985:354.6,353.967743:321.6,355.089111:116,357.080902:913.9,358.090057:355.9,359.206848:596.8,360.493347:606.3,361.288788:849.9,362.364838:237,363.516296:305.6,364.316559:447.5,365.313507:360.2,366.439819:485.5,367.779388:421.7,370.281403:517.1,371.275177:1451,372.630859:396.2,373.751679:393.9,374.789001:251,375.836578:344.4,377.333008:1827,379.147736:713.2,380.303070:1770,381.331757:461.6,382.405792:469.5,383.498108:266.7,385.028870:1338,385.864777:701.2,386.976990:333.3,389.350128:1385,390.408508:1402,391.383972:619.4,392.311188:327.2,393.294525:761.6,394.224518:1452,395.353394:796.3,396.430756:752.9,397.294525:1980,398.216919:1037,399.417694:399.3,400.370056:484.7,401.413605:467.2,402.205872:753.7,403.401642:1865,404.348083:1575,405.333221:463.7,406.330658:338.3,407.482666:2118,410.836212:2161,411.497040:1040,412.382690:415.6,421.244873:1063,422.143280:224.4,424.334564:16.9,425.329620:124.6,428.670166:42.18,431.086426:41.6,431.956207:69.96,433.171082:135.1,436.550140:154.6,440.234985:80.26,441.536957:298.8,442.292542:125.4,443.165619:326.4,444.222351:90.45,446.308716:71.8,447.000885:117.7,448.068970:46.04,449.165588:16.3,450.282623:58.95,451.363739:239.4,452.701752:396.4,453.843201:71.43,455.521851:103,456.264893:30.18,457.359100:329.9,458.313629:275.2,459.438477:53.76,460.566315:224,461.327118:161.8,462.182037:179.8,463.192871:336.1,464.124970:439.8,466.093353:300.5,467.280762:146.9,467.968048:54.96,469.086334:50.29,471.352447:620.4,472.582367:127.6,473.412720:34.68,474.616974:285.4,475.340240:107.8,476.298706:92.38,478.010803:163,478.804016:140.2,480.002502:188.1,481.067871:177.3,482.350189:23.42,483.684174:154.2,484.507202:346.2,485.254059:259.7,486.684692:71.25,487.641449:46.96,488.265533:41.01,491.267212:761.8,492.042053:388.9,493.069763:129.2,493.925629:54.47,495.201508:659.7,496.624176:130.9,497.280518:187.1,499.098846:35.05,500.754944:718.3,503.481445:548.6,504.361969:147,505.143036:22.82,506.285583:208.4,507.133423:266.4,508.178650:467.1,508.930145:77.74,510.259216:83.25,511.089447:144.4,512.814270:161.8,514.526978:251.3,515.600403:595.8,516.262695:335.8,518.145264:406.4,518.938293:363.4,520.011841:203.2,520.848389:268.5,521.601379:98.84,522.724243:72.78,527.262817:554.4,528.525757:105.5,530.003845:184,531.487488:137.6,532.251526:211.7,533.170105:301.7,534.228210:284.6,535.424805:340.7,536.352722:32.73,537.719971:69.9,538.493103:45.12,539.341309:162.8,540.428101:117.4,543.330872:177.1,544.218750:50.95,545.246460:154.5,546.295166:444.5,547.285584:224.4,548.140259:147.5,549.544678:132.7,553.311523:275.5,554.352112:48.45,555.350586:136.4,556.489990:574.1,558.289856:122.3,559.359070:154.6,560.308289:149.9,561.428955:144.8,562.536926:237.7,563.661743:270.4,564.437439:46.44,566.276856:233.6,567.308350:25.67,568.259949:44.18,569.530762:181.4,570.295837:67.04,571.206299:87.12,572.366882:151.1,573.285095:349.2,575.316834:261.9,576.300476:102.5,577.350708:592.9,578.842163:506.3,580.309387:516.4,581.341980:296,582.450317:455.9,583.449585:33.43,585.360840:60.9,586.982483:262.3,588.197266:378.8,589.520264:459.9,590.306641:577.7,591.383118:414.2,592.233459:64.48,593.187317:132.6,594.399353:67.65,595.392761:50.62,597.263123:41.83,598.634766:95.64,599.353638:179.7,600.495728:123.9,601.422241:150.3,604.355103:272.2,605.296997:130.5,606.369568:231.3,607.364502:198.8,608.218140:172.2,609.381043:96.59,611.355225:91.63,615.268372:29.11,616.448914:57.29,617.335815:154.8,618.351196:262.8,620.026184:320.2,621.128662:267.3,622.398560:188.1,624.169617:190,626.358826:163.2,627.585938:182.6,628.461121:143.1,629.269226:71.98,630.363037:148.4,632.337097:120.2,633.428894:48.59,636.138550:239.1,637.438782:46.33,638.519043:109,639.383301:141.7,640.389404:159.9,641.352234:186.5,642.386597:82.7,643.299560:47.86,644.375488:85.03,645.343872:186.1,646.305603:46.15,647.198914:64.92,648.453857:146,649.337280:40.11,650.409241:255,651.408447:207,652.395142:126.6,653.279297:88.15,654.340271:23.93,656.361450:168.4,657.258667:108.9,658.330322:68.11,659.415100:173.4,662.257080:110.2,663.213562:114.9,664.335327:19.71,666.277100:166,667.319397:88.3,669.166626:66.14,670.276550:33.21,671.245056:184.7,672.297974:173.9,673.595215:201.9,675.483215:309.1,676.364563:129,677.353394:191.9,678.356079:176.7,680.416504:75.58,682.025147:38.86,683.348755:30.6,684.302307:68.09,685.386536:254.2,686.480896:300.3,689.260010:393.4,691.276428:39.67,695.846985:66.73,696.573425:20.5,700.304504:44.5,703.443970:349.3,707.436584:71.49,708.236694:27.5,712.370117:20.8,713.515808:32.27,717.406311:34.71,718.130554:52.97,719.323731:263.2,720.484436:126.1,721.433166:72.68,723.382813:60.96,724.383911:161.3,725.459228:152.7,726.357483:49.3,727.432190:24.52,728.984131:32.86,732.600891:78.2,734.760925:27.41,735.389771:31.16,736.359375:101.6,739.518372:52.57,741.271362:39.53,744.455017:60.47,749.017822:83.37,750.384582:145.6,751.315918:62.09,757.393616:134.1,758.327759:156.7,763.292358:12.27,770.487549:211,772.507629:88.17,775.409058:175.1,776.460022:146.3,777.214600:62.94,783.514221:59.42,785.095886:22.68,786.271668:20.74,788.459351:130.2,793.782654:158.1,804.438110:25.05,807.746399:28.33,814.113037:68.52,817.378296:17.47,818.513367:28.9,852.438721:34.37,853.293640:84.84,854.517334:20.47 > --gc0p4Jq0M2Yt08jU534c0p > Content-Type: application/x-Mascot; name="query397" > > > And here is the result with the "TPP mgf files": > > title=300_19_01_F1P1NS_130402_01%2e27409%2e27409%2e2 > scans=27409 > rtinseconds=6372.73 > charge=2+ > mass_min=169.186300 > mass_max=1168.574700 > int_min=3 > int_max=1.064e+004 > num_vals=805 > num_used1=-1 > > Ions1=190.137500:182,336.150900:1643,461.308300:1373,539.576000:697,583.889700:1.064e+004,740.202900:211,823.450300:271,946.729600:318,990.665300:290,1161.418200:21,266.966800:145,364.280100:890,418.296900:1215,561.870800:697,575.324200:6263,689.364700:173,858.668300:243,916.574400:269,1017.731000:219,1069.737800:20,221.139700:94,314.278700:340,433.368200:392,501.683600:688,583.065900:5987,677.548800:158,814.631300:231,902.561200:207,1001.630800:185,1114.649800:17,261.192300:82,279.183300:277,464.567200:328,509.566700:638,574.145300:3562,696.595800:115,802.625400:180,885.576700:132,1002.647700:166,1166.706900:17,258.325600:74,360.353900:174,392.250700:279,556.315800:585,582.196800:756,676.581500:107,770.514200:174,929.688600:125,1018.628200:149,1115.495200:16,177.149400:72,354.736700:145,443.132800:279,564.383600:467,570.397800:498,708.546900:92,797.580100:127,872.580400:117,1034.700700:118,1145.854500:15,233.110900:66,332.568200:131,420.921600:181,548.372400:460,576.475500:370,682.242200:91,861.492100:108,871.538900:116,973.404100:67,1071.723900:11,265.231300:64,310.665900:98,376.733900:177,546.406700:457,569.682000:319,690.427700:88,824.535200:91,889.653000:96,1008.639600:65,1116.534100:11,239.238400:61,346.189000:95,445.281700:158,520.487100:348,577.567700:301,726.487200:77,796.375500:86,895.539200:95,1000.654100:63,1153.080400:11,200.826600:55,293.208800:90,427.289900:148,508.600200:343,591.393200:190,671.460100:75,771.500600:85,898.530900:72,1019.604500:52,1168.574700:11,169.186300:4,170.072500:5,173.134000:18,178.133500:10,179.957200:4,181.140800:7,182.105600:39,183.026300:35,184.064000:49,185.431500:20,186.118000:14,187.176000:5,188.992900:18,191.219400:7,192.131600:6,193.184900:9,195.148800:31,196.163500:6,197.217000:9,198.189500:13,199.155900:12,201.496800:7,202.177800:7,204.289700:10,205.150700:18,205.987300:6,207.966900:3,209.133000:33,210.284100:9,211.280300:38,212.181600:4,213.168800:8,214.108500:36,215.087500:45,216.086900:10,217.147800:6,218.104200:9,219.199600:20,220.082200:8,222.179900:35,223.101600:22,224.161000:10,225.193500:13,226.150400:17,227.117200:16,228.177800:17,229.336800:25,230.150400:14,231.110100:22,235.391100:44,236.218600:35,237.202300:6,238.270900:5,240.223400:12,241.249100:10,242.176600:12,243.229400:10,244.530700:39,245.327700:21,247.151600:15,248.154100:8,249.178200:19,250.230900:5,251.092600:30,252.200900:10,253.275600:8,254.122300:29,255.204200:7,256.179100:28,257.354500:24,259.298400:11,260.224100:28,262.225100:12,263.148200:38,264.298000:42,268.209000:24,269.305800:22,270.234900:23,271.282600:6,272.269300:21,273.930700:35,275.219100:19,276.202100:19,277.210700:30,278.136500:6,280.175300:26,281.164300:6,282.189400:31,283.190600:46,284.185900:33,285.137800:21,286.181100:18,288.329800:77,289.160100:64,290.257800:26,291.180100:14,292.504300:20,294.187200:58,295.342800:49,296.215600:24,297.116100:15,298.252400:22,299.258800:6,300.210800:28,301.095000:34,302.106100:61,303.220400:32,304.322400:70,305.286600:37,306.294500:10,307.196500:10,308.214000:13,309.246300:74,311.332200:33,313.212500:59,315.244900:34,316.384200:25,317.738000:84,319.155000:12,320.087100:36,321.333700:38,322.195900:33,323.380600:23,324.254100:40,326.040700:29,327.344400:23,328.224500:56,329.214400:25,330.349900:48,331.144800:8,333.362900:13,334.249000:29,337.117400:58,338.092300:11,339.491800:32,341.193300:19,342.242600:41,343.116900:9,344.230700:58,345.188100:34,347.314700:30,348.246900:71,349.299900:30,350.305800:30,351.320200:51,352.232000:14,353.326600:81,356.005100:40,357.309600:35,358.296000:83,359.303800:21,361.287400:44,362.278700:43,363.290700:43,365.265400:81,366.409500:39,367.593800:79,368.326500:24,369.462500:31,370.254700:19,371.306400:77,372.186200:33,373.369700:43,374.315600:84,375.433400:70,378.146600:24,379.486900:37,380.354200:46,381.303600:106,382.305000:39,383.273300:58,384.388200:20,385.462700:34,386.389900:31,387.130800:17,388.280600:42,389.486000:9,390.337300:31,391.225300:43,393.171300:48,394.315900:80,395.302700:20,396.230800:18,397.523600:35,398.556500:133,399.294600:33,400.461100:64,401.388300:75,402.332000:59,403.328400:26,404.360500:47,405.247000:18,406.456800:28,407.217700:20,408.308700:36,409.648500:76,410.454800:69,411.312200:72,412.432600:35,413.345900:29,414.266900:31,415.346300:107,416.239100:131,417.332300:69,419.487200:83,420.200600:61,421.652300:9,422.257300:37,423.315600:40,424.299400:55,425.173000:15,426.075900:31,428.300800:21,429.260700:50,430.411700:86,431.471700:19,432.402500:65,434.249300:82,435.591200:105,436.435300:102,437.244400:28,438.300000:68,439.554600:29,440.293000:21,441.334400:41,442.234700:71,444.240300:89,446.352500:79,447.299000:89,448.276500:43,449.291000:57,450.279500:119,451.330800:142,452.032700:14,452.744600:5,453.454100:49,454.342200:106,455.538100:49,456.505100:37,457.549200:99,458.339900:106,459.342500:111,460.440100:121,462.268800:68,463.227800:92,465.341500:57,466.327600:30,467.207200:62,468.318600:53,469.543600:36,470.392500:51,471.3464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> --gc0p4Jq0M2Yt08jU534c0p > Content-Type: application/x-Mascot; name="query4327" > > The difference lies in the title and in the scan info (that is missing in > the "MSconvert mgf" .dat file. > > So my questions are: > -Why the .dat coming from the MSconvert ans TPP convert don't have the > same structure? > -How could I solve my problem: getting the spectrum name instead of the > date in the pepxml file? > > Thanks in advance for any help. > > Delphine > > > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
