Re: [Psidev-pi-dev] Fragment ion information

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For your info, here is the format we use in Phenyx to explicitely 
annotate a spectrum (the most verbose but selfconsistent mode):

      <ionicSeries>
        <oneIonicSeries fragType='a'>
          <expTheoSpectraMatch len='14'>

<expMoz>120.0761:221.1184:-1:-1:-1:664.287:777.3536:905.5523:-1:-1:-1:-1:-1:-1</expMoz>

<expIntensity>3.1905:13.0476:-1:-1:-1:3.1905:4.2857:7.7619:-1:-1:-1:-1:-1:-1</expIntensity>

<expIntensitySlice>1:4:-1:-1:-1:1:2:3:-1:-1:-1:-1:-1:-1</expIntensitySlice>

<theoMass>120.0478:221.0954:336.1224:464.181:593.2236:664.2607:777.3447:905.4033:1020.43:1133.514:1319.594:1447.652:1633.731:1789.833</theoMass>

<deltaMass>-0.02834:-0.02296:-9999:-9999:-9999:-0.02634:-0.00888:-0.149:-9999:-9999:-9999:-9999:-9999:-9999</deltaMass>
          </expTheoSpectraMatch>
        </oneIonicSeries>
        <oneIonicSeries fragType='a-NH3'>
          <expTheoSpectraMatch len='14'>

<expMoz>-1:-1:-1:-1:576.2927:647.3032:-1:-1:-1:-1:-1:-1:-1:-1</expMoz>

<expIntensity>-1:-1:-1:-1:4.8571:4.2857:-1:-1:-1:-1:-1:-1:-1:-1</expIntensity>

<expIntensitySlice>-1:-1:-1:-1:2:2:-1:-1:-1:-1:-1:-1:-1:-1</expIntensitySlice>

<theoMass>-1:-1:-1:447.1438:576.1864:647.2235:760.3076:888.3662:1003.393:1116.477:1302.556:1430.615:1616.694:1772.795</theoMass>

<deltaMass>-9999:-9999:-9999:-9999:-0.10627:-0.07966:-9999:-9999:-9999:-9999:-9999:-9999:-9999:-9999</deltaMass>
          </expTheoSpectraMatch>
        </oneIonicSeries>
        <oneIonicSeries fragType='b'>
          <expTheoSpectraMatch len='14'>

<expMoz>-1:249.1126:-1:492.2127:621.29:692.3133:805.4106:-1:1048.536:1161.645:1347.596:-1:-1:-1</expMoz>

<expIntensity>-1:39.9048:-1:13.6667:34.4762:27.0952:15.5238:-1:4.2857:4.2857:1.6667:-1:-1:-1</expIntensity>

<expIntensitySlice>-1:4:-1:4:4:4:4:-1:2:2:0:-1:-1:-1</expIntensitySlice>

<theoMass>148.0427:249.0904:364.1173:492.1759:621.2185:692.2556:805.3396:933.3982:1048.425:1161.509:1347.589:1475.647:1661.726:1817.828</theoMass>

<deltaMass>-9999:-0.02225:-9999:-0.03683:-0.07154:-0.05773:-0.07097:-9999:-0.11075:-0.13559:-0.00708:-9999:-9999:-9999</deltaMass>
          </expTheoSpectraMatch>
        </oneIonicSeries>
        <oneIonicSeries fragType='b-H2O'>
          <expTheoSpectraMatch len='14'>

<expMoz>-1:231.1091:346.1367:474.213:603.2585:674.29:787.4133:915.475:1030.526:1143.635:-1:-1:-1:-1</expMoz>

<expIntensity>-1:7.5238:5.7619:11.5714:8.5714:17.2857:15.7619:3.9524:5.7143:8.2381:-1:-1:-1:-1</expIntensity>

<expIntensitySlice>-1:3:3:4:3:4:4:1:3:3:-1:-1:-1:-1</expIntensitySlice>

<theoMass>-1:231.0798:346.1067:474.1653:603.2079:674.245:787.3291:915.3877:1030.415:1143.499:1329.578:1457.637:1643.716:1799.817</theoMass>

<deltaMass>-9999:-0.02931:-0.02997:-0.04769:-0.0506:-0.04499:-0.08423:-0.08735:-0.11141:-0.13615:-9999:-9999:-9999:-9999</deltaMass>
          </expTheoSpectraMatch>
        </oneIonicSeries>
        <oneIonicSeries fragType='b-NH3'>
          <expTheoSpectraMatch len='14'>

<expMoz>-1:-1:-1:475.2086:604.242:675.3962:788.4813:-1:1031.562:1144.459:-1:-1:-1:-1</expMoz>

<expIntensity>-1:-1:-1:5.2381:7.7619:61.2857:43.0476:-1:99.0952:5.7619:-1:-1:-1:-1</expIntensity>

<expIntensitySlice>-1:-1:-1:2:3:4:4:-1:4:3:-1:-1:-1:-1</expIntensitySlice>

<theoMass>-1:-1:-1:475.1388:604.1813:675.2184:788.3025:916.3611:1031.388:1144.472:1330.551:1458.61:1644.689:1800.79</theoMass>

<deltaMass>-9999:-9999:-9999:-0.06985:-0.06066:-0.17775:-0.17879:-9999:-0.17447:0.01319:-9999:-9999:-9999:-9999</deltaMass>
          </expTheoSpectraMatch>
        </oneIonicSeries>
        <oneIonicSeries fragType='y'>
          <expTheoSpectraMatch len='14'>

<expMoz>-1:-1:1587.914:1472.891:1344.755:1215.739:1144.677:1031.562:903.5342:788.4813:675.3962:489.3123:361.2253:175.147</expMoz>

<expIntensity>-1:-1:5.7619:8.6667:20.4286:48.0952:44.1429:99.0952:39.8095:43.0476:61.2857:53.9524:55.6191:26.2381</expIntensity>

<expIntensitySlice>-1:-1:3:3:4:4:4:4:4:4:4:4:4:4</expIntensitySlice>

<theoMass>1835.838:1688.803:1587.755:1472.728:1344.67:1215.627:1144.59:1031.506:903.4472:788.4202:675.3362:489.2569:361.1983:175.119</theoMass>

<deltaMass>-9999:-9999:-0.1593754:-0.1626154:-0.0849954:-0.1118854:-0.0871954:-0.0567554:-0.0870354:-0.0610754:-0.0600354:-0.0554454:-0.0270254:-0.0280354</deltaMass>
          </expTheoSpectraMatch>
        </oneIonicSeries>
        <oneIonicSeries fragType='y-H2O'>
          <expTheoSpectraMatch len='14'>
            <expMoz>-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1</expMoz>

<expIntensity>-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1</expIntensity>

<expIntensitySlice>-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1</expIntensitySlice>

<theoMass>1817.828:1670.792:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1:-1</theoMass>

<deltaMass>-9999:-9999:-9999:-9999:-9999:-9999:-9999:-9999:-9999:-9999:-9999:-9999:-9999:-9999</deltaMass>
          </expTheoSpectraMatch>
        </oneIonicSeries>
        <oneIonicSeries fragType='y-NH3'>
          <expTheoSpectraMatch len='14'>

<expMoz>-1:-1:-1:1455.827:-1:1198.736:-1:1014.542:-1:771.4312:658.3353:472.3802:344.1792:-1</expMoz>

<expIntensity>-1:-1:-1:6.5238:-1:5.2857:-1:6.619:-1:3.0952:10.2857:1.3333:4.1905:-1</expIntensity>

<expIntensitySlice>-1:-1:-1:3:-1:2:-1:3:-1:1:3:0:2:-1</expIntensitySlice>

<theoMass>1818.801:1671.766:1570.718:1455.691:1327.632:1198.59:1127.553:1014.469:886.41:771.3831:658.299:472.2197:344.1612:158.0818</theoMass>

<deltaMass>-9999:-9999:-9999:-0.1364354:-9999:-0.1462054:-9999:-0.0735754:-9999:-0.0480954:-0.0362554:-0.1604654:-0.0180454:-9999</deltaMass>
          </expTheoSpectraMatch>
        </oneIonicSeries>
        <extraFragSerie fragType='immonium ions'>
            <expMoz>-1:-1:-1:-1:-1:101.0882:-1:-1:-1:-1</expMoz>
            <expIntensity>-1:-1:-1:-1:-1:3.1905:-1:-1:-1:-1</expIntensity>

<expIntensitySlice>-1:-1:-1:-1:-1:1:-1:-1:-1:-1</expIntensitySlice>

<theoMass>44.02621:74.03678:86.07316:86.07316:88.01604:101.0477:102.0317:104.0296:129.0902:159.0684</theoMass>

<deltaMass>-9999:-9999:-9999:-9999:-9999:-0.04052:-9999:-9999:-9999:-9999</deltaMass>
            <label>A:T:I:L:D:Q:E:M:R:W</label>

<sequencePosition>-1:-1:-1:-1:-1:-1:-1:-1:-1:-1</sequencePosition>
        </extraFragSerie>
        <extraFragSerie fragType='precursor'>
            <expMoz>918.475:-1</expMoz>
            <expIntensity>17.7619:-1</expIntensity>
            <expIntensitySlice>4:-1</expIntensitySlice>
            <theoMass>918.4227:1835.838</theoMass>
            <deltaMass>-0.0523127:-9999</deltaMass>
            <label>2+:1+</label>
            <sequencePosition>-1:-1</sequencePosition>
        </extraFragSerie>
      </ionicSeries>

Pierre-Alain

Lennart Martens wrote:
> (ooops, I originally only sent this to David rather than the whole list. 
> Corrected here).
>
> Hi David,
>
>
>  >  >>> Let the argument (re-)commence!
>  > Good to hear from you - maybe ;)
>
> Always glad to help :) .
>
>
>  > Just to clarify, without this, there is no information haemorrhaging. 
>  > It's just rather hard to reconstruct some of the information... which 
>  > you may say is the same thing.
>
> Yes, I'd say it's the same thing. If something is difficult, nobody (or 
> practically nobody) will expend the effort to do it, and many (like 
> myself) will simply sit in a corner and complain about how difficult it 
> is to do this. Finally, some of those who do decide to do something will 
> do it badly.
>
>  > What's the problem with a separate to tool to generate the 
> information > from the (less huge) anaylsisXML file and the mzML file?
>
> I can come up with three reasons right now:
>   i) that the tool may not exist (anymore);
>   ii) that the tool may not be up-to-date (or may be too up-to-date, 
> pick and choose which one you like); and
>   iii) that the information is no longer atomic (I'd need access to both 
> the file and the tool to get all relevant information).
>
>
> Cheers,
>
> lnnrt.
>
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