Re: [Psidev-ms-dev] <precursor msLevel="1" or msLevel="2" for msms data in the mzdata format (LTQ d

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Hi Alex,
Yes, it's definitely incorrect. I'll pass on the message to the 
appropriate person and I'm confident they will fix it in a future 
release. I'm not aware of any other mzData producers doing it this way.

David Creasy.

Brian Pratt wrote:
> I agree, that doesn't make sense.  It sounds like there's a bug in the module that wrote the data.
> 
> - Brian Pratt
> www.insilicos.com
> 
>> -----Original Message-----
>> From: psi...@li... 
>> [mailto:psi...@li...] On 
>> Behalf Of Alexandre Masselot
>> Sent: Thursday, September 28, 2006 6:10 AM
>> To: psi...@li...
>> Subject: [Psidev-ms-dev] <precursor msLevel="1" or 
>> msLevel="2" for msms data in the mzdata format (LTQ data)
>>
>> Hello,
>> something raised a problem in our code and into my understanding of
>> mzdata format for msms peaklist
>>
>> We have been writing (and still writing...) some  opensource 
>> perl module
>> InSilicoSpectro (CPAN & http://insilicospectro.vital-it.ch), 
>> which does,
>> among plenty of other things MS peaklist conversion from/to 
>> various formats
>>
>> In demo file, spectrumentInstrument is set to msLevel="2", then the
>> precursor info is set msLevel="1", which can seems logical.
>>
>> Then I have some LTQ data
>> spectrumentInstrument still msLevel="2", then precursor msLevel="2",
>> which either follows an other logic, no?
>>
>> This happen for all the spectra in each files.
>>
>> Anyone could give me some light would be very welcome,
>>
>> Thanks in advance
>> Alex
>>
>>
>>       myo_ms2_1.05
>>
>>     <spectrum id="3">
>>             <spectrumDesc>
>>                 <spectrumSettings>
>>                     <acqSpecification spectrumType="discrete"
>> methodOfCombination="sum" count="1">
>>                         <acquisition acqNumber="3"/>
>>                     </acqSpecification>
>>                     <spectrumInstrument *msLevel="2"
>> *mzRangeStart="100.000000" mzRangeStop="1350.000000">
>>                         <cvParam cvLabel="psi" accession="PSI:1000036"
>> name="ScanMode" value="MassScan"/>
>>                         <cvParam cvLabel="psi" accession="PSI:1000037"
>> name="Polarity" value="Positive"/>
>>                         <cvParam cvLabel="psi" accession="PSI:1000038"
>> name="TimeInMinutes" value="0.045000"/>
>>                         <userParam name="ScanType" value="full"/>
>>                     </spectrumInstrument>
>>                 </spectrumSettings>
>>                 <precursorList count="1">
>>                     <precursor *msLevel="1" *spectrumRef="1">
>>                         <ionSelection>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000040" name="MassToChargeRatio" value="334.82"/>
>>                         </ionSelection>
>>                         <activation>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000044" name="Method" value="CID"/>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000045" name="CollisionEnergy" value="28.00"/>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000046" name="EnergyUnits" value="Percent"/>
>>                         </activation>
>>                     </precursor>
>>                 </precursorList>
>>             </spectrumDesc>
>>             <mzArrayBinary>
>>                 <data precision="32" endian="little"
>> length="77">+hMVQ1A1K0NGFjFDmBQ5QzxKPUPc/UpDLhJPQ6jrVkMEol1D/G
>> heQygoYUNOHmdD/kloQyjwaEPm8WpDcDx2Q8otd0O6PXhDICJ7QzCjfUPYfH9D
>> kAeDQ/CHiEOI8YhDqmSJQ5TeiUOYUIxDmByPQ+iSj0Pa9Y9DYHCQQzAtkUMIe5
>> FDGNSRQ0RDkkMkxJJDdDqTQzACl0OQj5dDdOmXQzhzmENs1ZhDzmiZQ7DOmUM4
>> RZpDMAGbQ0h1m0MU2ptDSDqcQ0TFnUN8Mp5DSqGeQ9gdn0O+0J9D0HygQwLuoE
> PiMKJDctqjQxiwpEOcDaVDgIemQ1D/pkPEfadDpP2nQ4hmq0PA/6xDdOmtQ8gKr0PEM7BDysqwQzg4sUOcZ7ND7Ni4Qyo+uU> PClblD2DzmQ+gH8UM=</data>
>>             </mzArrayBinary>
>>             <intenArrayBinary>
>>                 <data precision="32" endian="little"
>> length="77">ALBORQCAC0QAYDNFAOCoRAAABkUAIOJEAADbRABgkkUAMFxFAJ
> AnRQCAjkQAgChEAKBoRQAQeUYAAAFEAIA/RADAPEQAoIdEAKDqRABACUUAABFEAADTRAAO2UYAwE1EwHJgSAA8HkYAgGhEAA>
> AnRACAeUUAyNtFAPwkRgAW6kYA0F9GAD+tR8B6k0gAHo1GAEAcRADgZUUAIFZF
>> AJAKRQDAh0YA4KFFAAh3RgCZBkcAMAdFAHixRQAAakQA6L1FAGC9RQBmpUYAAM
>> 5EAMiuRQAAcEQAoLhEAFAmRQAAtkQA4BlFANBVRQBAAkQAALNDAPxnRgDQvUUA
>> oKlFAOBNRQBAMUUAsCpFAAC2RADAWkQAEIZFAJDQRQCwCUUAAGpEABB/RQDAlk
>> QAwEBEAIDsQwDANUQ=</data>
>>             </intenArrayBinary>
>>         </spectrum>
>>
>>
>>       LTQ exported mzdata
>>
>>
>> <spectrum id="2">
>>             <spectrumDesc>
>>                 <spectrumSettings>
>>                     <acqSpecification
>> spectrumType="CentroidMassSpectrum" methodOfCombination="sum" 
>> count="1">
>>                         <acquisition acqNumber="2"/>
>>                     </acqSpecification>
>>                     <spectrumInstrument *msLevel="2"*
>> mzRangeStart="110.000000" mzRangeStop="910.000000">
>>                         <cvParam cvLabel="psi" accession="PSI:1000036"
>> name="ScanMode" value="MassScan"/>
>>                         <cvParam cvLabel="psi" accession="PSI:1000037"
>> name="Polarity" value="Positive"/>
>>                         <cvParam cvLabel="psi" accession="PSI:1000038"
>> name="TimeInMinutes" value="14.002800"/>
>>                         <cvParam cvLabel="psi" accession="PSI:1000035"
>> name="PeakProcessing" value="ContinuumMassSpectrum"/>
>>                     </spectrumInstrument>
>>                 </spectrumSettings>
>>                 <precursorList count = "1">
>>                     <precursor *msLevel="2"* spectrumRef="1">
>>                         <ionSelection>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000040" name="MassToChargeRatio" value="449.728607"/>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000041" name="ChargeState" value="2"/>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000041" name="ChargeState" value="3"/>
>>                         </ionSelection>
>>                         <activation>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000044" name="Method" value="CID"/>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000045" name="CollisionEnergy" value="35.00"/>
>>                         </activation>
>>                     </precursor>
>>                 </precursorList>
>>             </spectrumDesc>
>>             <mzArrayBinary>
>>                 <data precision="64" endian="little"
>> length="26">AAAAgHL8aEAAAADANSppQAAAAMBNAWxAAAAAANhdbEAAAAAAch
> lwQAAAAOBez3FAAAAAwHsSckAAAACAKkJzQAAAAADZEnVAAAAAQDCQdUAAAADg4AR2QAAAAMBrhnZAAAAAAJdNd0AAAABgUp>
> B3QAAAAOA1sHdAAAAAQGWReEAAAACAUyx6QAAAAAACanpAAAAAIMSgekAAAABg
>> h+F6QAAAAOCg9HpAAAAAoL8Be0AAAADgphN7QAAAAOAUhHtAAAAAILUifEAAAA
>> BgRjt9QA==</data>
>>             </mzArrayBinary>
>>             <intenArrayBinary>
>>                 <data precision="64" endian="little"
>> length="26">AAAAYA24EkAAAAAASOjmPwAAAEAcNOs/AAAAIHZw4z8AAACAIQ
> T7PwAAAEB8qxNAAAAAAPF5D0AAAACg6X3/PwAAAMC/> +BFAAAAA4JNY7z8AAAAgKVznPwAAAMCfQvI/AAAAoDyfFUAAAABghBLpPwAAAM
>> AoJgFAAAAAYOGaGkAAAABgf5AYQAAAAMBj6gJAAAAAYHv/6T8AAADgiaUFQAAA
>> AAAb2jJAAAAA4D06IEAAAABACm9BQAAAAGBbqRVAAAAAoLdPBUAAAABgNsjpPw
>> ==</data>
>>             </intenArrayBinary>
>>         </spectrum>
>>         <spectrum id="3">
>>             <spectrumDesc>
>>                 <spectrumSettings>
>>                     <acqSpecification
>> spectrumType="CentroidMassSpectrum" methodOfCombination="sum" 
>> count="1">
>>                         <acquisition acqNumber="3"/>
>>                     </acqSpecification>
>>                     <spectrumInstrument *msLevel="2"*
>> mzRangeStart="95.000000" mzRangeStop="795.000000">
>>                         <cvParam cvLabel="psi" accession="PSI:1000036"
>> name="ScanMode" value="MassScan"/>
>>                         <cvParam cvLabel="psi" accession="PSI:1000037"
>> name="Polarity" value="Positive"/>
>>                         <cvParam cvLabel="psi" accession="PSI:1000038"
>> name="TimeInMinutes" value="14.015817"/>
>>                         <cvParam cvLabel="psi" accession="PSI:1000035"
>> name="PeakProcessing" value="ContinuumMassSpectrum"/>
>>                     </spectrumInstrument>
>>                 </spectrumSettings>
>>                 <precursorList count = "1">
>>                     <precursor *msLevel="2"* spectrumRef="2">
>>                         <ionSelection>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000040" name="MassToChargeRatio" value="391.069244"/>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000041" name="ChargeState" value="2"/>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000041" name="ChargeState" value="3"/>
>>                         </ionSelection>
>>                         <activation>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000044" name="Method" value="CID"/>
>>                             <cvParam cvLabel="psi"
>> accession="PSI:1000045" name="CollisionEnergy" value="35.00"/>
>>                         </activation>
>>                     </precursor>
>>                 </precursorList>
>>             </spectrumDesc>
>>             <mzArrayBinary>
>>                 <data precision="64" endian="little"
>> length="85">AAAAQAo8XkAAAABgK8FeQAAAAABoWWBAAAAAoGKlYEAAAAAAzy
> NhQAAAAMAHVmFAAAAAoD+eYUAAAADAzONhQAAAACAwnmJAAAAAIHzcYkAAAADAkv5iQAAAACC9j2NAAAAAYBEkZEAAAADAZN>
> 1kQAAAAGCnnmVAAAAAgJTiZUAAAADA3QJmQAAAAECVOmdAAAAAwGJPZ0AAAABA
>> XBhoQAAAAKASnGlAAAAAoMPgaUAAAACAG1tqQAAAAACIKGtAAAAAALOra0AAAA
>> CAOdxrQAAAAIAPIWxAAAAAALw2bEAAAADAtppsQAAAACCXvWxAAAAAQOWebUAA
>> AADgUeNtQAAAAGBkUG5AAAAAwCBkb0AAAABgmt9vQAAAAACVL3BAAAAAALhAcE
>> AAAABg6UtwQAAAAADAVXBAAAAAQH9ucEAAAABA0pBwQAAAACAG83BAAAAAYKYL
>> cUAAAAAA1iZxQAAAAABEMXFAAAAA4IlQcUAAAAAAWHBxQAAAAOBfjnFAAAAAgO
>> EMckAAAACA5pFyQAAAAECoqXJAAAAA4AjzckAAAACAwDdzQAAAAOA7k3NAAAAA
>> wCSmc0AAAAAAW8FzQAAAAIBSDHRAAAAAIIlWdEAAAABAaWB0QAAAAMAqj3RAAA
>> AAAH6hdEAAAABAJDx1QAAAAADEk3VAAAAAgPCxdUAAAACAKL51QAAAAAAo8XVA
>> AAAAIJ+kdkAAAABgwLp2QAAAAMDAAHdAAAAAQPNBd0AAAACg7k93QAAAAMCPW3
>> dAAAAAADBld0AAAACgvuR3QAAAAED5fnhAAAAAwIXkeEAAAABgT4t5QAAAACBv
>> jHpAAAAAwBcSfUAAAABgOpN9QAAAACDxpH5AAAAAgBlsgUAAAACAV8GBQAAAAA
>> DUFYJAAAAAwJYshEA=</data>
>>             </mzArrayBinary>
>>             <intenArrayBinary>
>>                 <data precision="64" endian="little"
>> length="85">AAAAwMPJAUAAAABArr70PwAAAMD/xgBAAAAAoH+3/D8AAACgkT
> 4LQAAAAICGFhNAAAAAIFnSG0AAAADgCTflPwAAAMAIB29AAAAA4IQHM0AAAAAg3CwDQAAAAOCtROM/AAAAYPO15z8AAADApR>
> 9IQAAAAICUefg/AAAAQMlXMUAAAAAg8krxPwAAAEDJavk/AAAAIAaR8T8AAABA
>> uVEkQAAAAMCItglAAAAAwGV95z8AAACAF9o4QAAAAMCmzQ5AAAAAIPfSAUAAAA
>> AAsnwaQAAAAEBm+e0/AAAAgG4sAEAAAAAg0Sw7QAAAAADCngVAAAAAgFatB0AA
>> AABA5fTsPwAAAAD2lARAAAAAYFmJEEAAAADAAo4xQAAAAMBx1QJAAAAAQNaQNE
>> AAAABgJoNTQAAAAGCvGCRAAAAAwBaGIUAAAABAjE36PwAAAADyNQBAAAAAoKzt
>> IkAAAACAlW/tPwAAAIBRJO8/AAAAYNy5CUAAAABAhiBaQAAAAIDzvgpAAAAA4B
>> zgA0AAAADg3CbyPwAAAOB7xw5AAAAAAImSI0AAAAAgdOwQQAAAACAeuPo/AAAA
>> oGo07D8AAABg4JTzPwAAACBtRhVAAAAA4KLT9D8AAACAIQUhQAAAAODRDARAAA
>> AAACjGFkAAAADApNzpPwAAAEBNTvU/AAAAIBY9CEAAAABAfF0PQAAAAGBcPx1A
>> AAAAgDyQBEAAAACAMhf6PwAAAADboPI/AAAAgPUCFUAAAAAA4yA6QAAAAEDaqA
>> pAAAAAALA0BEAAAABgV+YwQAAAAACdvPY/AAAAIBdaAUAAAADgLFwJQAAAAECs
>> DQxAAAAAoDSWB0AAAAAASu0BQAAAAECuaBRAAAAAoN22IkAAAADAYNTxPwAAAG
>> D5xwJAAAAAINkzB0A=</data>
>>             </intenArrayBinary>
>>         </spectrum>
>>
>> -- 
>> Alexandre Masselot, phD
>> Senior bioinformatician
>> www.genebio.com
>> voice: +41 22 702 99 00
>>
>>
>>
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> 
> 
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-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
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*** please note change of address ***

Re: [Psidev-ms-dev] <precursor msLevel="1" or msLevel="2" for msms data in the mzdata format (LTQ d

Re: [Psidev-ms-dev] <precursor msLevel="1" or msLevel="2" for msms data in the mzdata format (LTQ data)