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

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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 forma=
ts

In demo file, spectrumentInstrument is set to msLevel=3D"2", then the
precursor info is set msLevel=3D"1", which can seems logical.

Then I have some LTQ data
spectrumentInstrument still msLevel=3D"2", then precursor msLevel=3D"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=3D"3">
            <spectrumDesc>
                <spectrumSettings>
                    <acqSpecification spectrumType=3D"discrete"
methodOfCombination=3D"sum" count=3D"1">
                        <acquisition acqNumber=3D"3"/>
                    </acqSpecification>
                    <spectrumInstrument *msLevel=3D"2"
*mzRangeStart=3D"100.000000" mzRangeStop=3D"1350.000000">
                        <cvParam cvLabel=3D"psi" accession=3D"PSI:1000036=
"
name=3D"ScanMode" value=3D"MassScan"/>
                        <cvParam cvLabel=3D"psi" accession=3D"PSI:1000037=
"
name=3D"Polarity" value=3D"Positive"/>
                        <cvParam cvLabel=3D"psi" accession=3D"PSI:1000038=
"
name=3D"TimeInMinutes" value=3D"0.045000"/>
                        <userParam name=3D"ScanType" value=3D"full"/>
                    </spectrumInstrument>
                </spectrumSettings>
                <precursorList count=3D"1">
                    <precursor *msLevel=3D"1" *spectrumRef=3D"1">
                        <ionSelection>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000040" name=3D"MassToChargeRatio" value=3D"334.82"/>
                        </ionSelection>
                        <activation>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000044" name=3D"Method" value=3D"CID"/>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000045" name=3D"CollisionEnergy" value=3D"28.00"/>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000046" name=3D"EnergyUnits" value=3D"Percent"/>
                        </activation>
                    </precursor>
                </precursorList>
            </spectrumDesc>
            <mzArrayBinary>
                <data precision=3D"32" endian=3D"little"
length=3D"77">+hMVQ1A1K0NGFjFDmBQ5QzxKPUPc/UpDLhJPQ6jrVkMEol1D/GheQygoYUN=
OHmdD/kloQyjwaEPm8WpDcDx2Q8otd0O6PXhDICJ7QzCjfUPYfH9DkAeDQ/CHiEOI8YhDqmSJ=
Q5TeiUOYUIxDmByPQ+iSj0Pa9Y9DYHCQQzAtkUMIe5FDGNSRQ0RDkkMkxJJDdDqTQzACl0OQj=
5dDdOmXQzhzmENs1ZhDzmiZQ7DOmUM4RZpDMAGbQ0h1m0MU2ptDSDqcQ0TFnUN8Mp5DSqGeQ9=
gdn0O+0J9D0HygQwLuoEPiMKJDctqjQxiwpEOcDaVDgIemQ1D/pkPEfadDpP2nQ4hmq0PA/6x=
DdOmtQ8gKr0PEM7BDysqwQzg4sUOcZ7ND7Ni4Qyo+uUPClblD2DzmQ+gH8UM=3D</data>
            </mzArrayBinary>
            <intenArrayBinary>
                <data precision=3D"32" endian=3D"little"
length=3D"77">ALBORQCAC0QAYDNFAOCoRAAABkUAIOJEAADbRABgkkUAMFxFAJAnRQCAjkQ=
AgChEAKBoRQAQeUYAAAFEAIA/RADAPEQAoIdEAKDqRABACUUAABFEAADTRAAO2UYAwE1EwHJg=
SAA8HkYAgGhEAAAnRACAeUUAyNtFAPwkRgAW6kYA0F9GAD+tR8B6k0gAHo1GAEAcRADgZUUAI=
FZFAJAKRQDAh0YA4KFFAAh3RgCZBkcAMAdFAHixRQAAakQA6L1FAGC9RQBmpUYAAM5EAMiuRQ=
AAcEQAoLhEAFAmRQAAtkQA4BlFANBVRQBAAkQAALNDAPxnRgDQvUUAoKlFAOBNRQBAMUUAsCp=
FAAC2RADAWkQAEIZFAJDQRQCwCUUAAGpEABB/RQDAlkQAwEBEAIDsQwDANUQ=3D</data>
            </intenArrayBinary>
        </spectrum>

      LTQ exported mzdata

<spectrum id=3D"2">
            <spectrumDesc>
                <spectrumSettings>
                    <acqSpecification
spectrumType=3D"CentroidMassSpectrum" methodOfCombination=3D"sum" count=3D=
"1">
                        <acquisition acqNumber=3D"2"/>
                    </acqSpecification>
                    <spectrumInstrument *msLevel=3D"2"*
mzRangeStart=3D"110.000000" mzRangeStop=3D"910.000000">
                        <cvParam cvLabel=3D"psi" accession=3D"PSI:1000036=
"
name=3D"ScanMode" value=3D"MassScan"/>
                        <cvParam cvLabel=3D"psi" accession=3D"PSI:1000037=
"
name=3D"Polarity" value=3D"Positive"/>
                        <cvParam cvLabel=3D"psi" accession=3D"PSI:1000038=
"
name=3D"TimeInMinutes" value=3D"14.002800"/>
                        <cvParam cvLabel=3D"psi" accession=3D"PSI:1000035=
"
name=3D"PeakProcessing" value=3D"ContinuumMassSpectrum"/>
                    </spectrumInstrument>
                </spectrumSettings>
                <precursorList count =3D "1">
                    <precursor *msLevel=3D"2"* spectrumRef=3D"1">
                        <ionSelection>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000040" name=3D"MassToChargeRatio" value=3D"449.728607"=
/>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000041" name=3D"ChargeState" value=3D"2"/>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000041" name=3D"ChargeState" value=3D"3"/>
                        </ionSelection>
                        <activation>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000044" name=3D"Method" value=3D"CID"/>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000045" name=3D"CollisionEnergy" value=3D"35.00"/>
                        </activation>
                    </precursor>
                </precursorList>
            </spectrumDesc>
            <mzArrayBinary>
                <data precision=3D"64" endian=3D"little"
length=3D"26">AAAAgHL8aEAAAADANSppQAAAAMBNAWxAAAAAANhdbEAAAAAAchlwQAAAAOB=
ez3FAAAAAwHsSckAAAACAKkJzQAAAAADZEnVAAAAAQDCQdUAAAADg4AR2QAAAAMBrhnZAAAAA=
AJdNd0AAAABgUpB3QAAAAOA1sHdAAAAAQGWReEAAAACAUyx6QAAAAAACanpAAAAAIMSgekAAA=
ABgh+F6QAAAAOCg9HpAAAAAoL8Be0AAAADgphN7QAAAAOAUhHtAAAAAILUifEAAAABgRjt9QA=
=3D=3D</data>
            </mzArrayBinary>
            <intenArrayBinary>
                <data precision=3D"64" endian=3D"little"
length=3D"26">AAAAYA24EkAAAAAASOjmPwAAAEAcNOs/AAAAIHZw4z8AAACAIQT7PwAAAEB=
8qxNAAAAAAPF5D0AAAACg6X3/PwAAAMC/+BFAAAAA4JNY7z8AAAAgKVznPwAAAMCfQvI/AAAA=
oDyfFUAAAABghBLpPwAAAMAoJgFAAAAAYOGaGkAAAABgf5AYQAAAAMBj6gJAAAAAYHv/6T8AA=
ADgiaUFQAAAAAAb2jJAAAAA4D06IEAAAABACm9BQAAAAGBbqRVAAAAAoLdPBUAAAABgNsjpPw=
=3D=3D</data>
            </intenArrayBinary>
        </spectrum>
        <spectrum id=3D"3">
            <spectrumDesc>
                <spectrumSettings>
                    <acqSpecification
spectrumType=3D"CentroidMassSpectrum" methodOfCombination=3D"sum" count=3D=
"1">
                        <acquisition acqNumber=3D"3"/>
                    </acqSpecification>
                    <spectrumInstrument *msLevel=3D"2"*
mzRangeStart=3D"95.000000" mzRangeStop=3D"795.000000">
                        <cvParam cvLabel=3D"psi" accession=3D"PSI:1000036=
"
name=3D"ScanMode" value=3D"MassScan"/>
                        <cvParam cvLabel=3D"psi" accession=3D"PSI:1000037=
"
name=3D"Polarity" value=3D"Positive"/>
                        <cvParam cvLabel=3D"psi" accession=3D"PSI:1000038=
"
name=3D"TimeInMinutes" value=3D"14.015817"/>
                        <cvParam cvLabel=3D"psi" accession=3D"PSI:1000035=
"
name=3D"PeakProcessing" value=3D"ContinuumMassSpectrum"/>
                    </spectrumInstrument>
                </spectrumSettings>
                <precursorList count =3D "1">
                    <precursor *msLevel=3D"2"* spectrumRef=3D"2">
                        <ionSelection>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000040" name=3D"MassToChargeRatio" value=3D"391.069244"=
/>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000041" name=3D"ChargeState" value=3D"2"/>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000041" name=3D"ChargeState" value=3D"3"/>
                        </ionSelection>
                        <activation>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000044" name=3D"Method" value=3D"CID"/>
                            <cvParam cvLabel=3D"psi"
accession=3D"PSI:1000045" name=3D"CollisionEnergy" value=3D"35.00"/>
                        </activation>
                    </precursor>
                </precursorList>
            </spectrumDesc>
            <mzArrayBinary>
                <data precision=3D"64" endian=3D"little"
length=3D"85">AAAAQAo8XkAAAABgK8FeQAAAAABoWWBAAAAAoGKlYEAAAAAAzyNhQAAAAMA=
HVmFAAAAAoD+eYUAAAADAzONhQAAAACAwnmJAAAAAIHzcYkAAAADAkv5iQAAAACC9j2NAAAAA=
YBEkZEAAAADAZN1kQAAAAGCnnmVAAAAAgJTiZUAAAADA3QJmQAAAAECVOmdAAAAAwGJPZ0AAA=
ABAXBhoQAAAAKASnGlAAAAAoMPgaUAAAACAG1tqQAAAAACIKGtAAAAAALOra0AAAACAOdxrQA=
AAAIAPIWxAAAAAALw2bEAAAADAtppsQAAAACCXvWxAAAAAQOWebUAAAADgUeNtQAAAAGBkUG5=
AAAAAwCBkb0AAAABgmt9vQAAAAACVL3BAAAAAALhAcEAAAABg6UtwQAAAAADAVXBAAAAAQH9u=
cEAAAABA0pBwQAAAACAG83BAAAAAYKYLcUAAAAAA1iZxQAAAAABEMXFAAAAA4IlQcUAAAAAAW=
HBxQAAAAOBfjnFAAAAAgOEMckAAAACA5pFyQAAAAECoqXJAAAAA4AjzckAAAACAwDdzQAAAAO=
A7k3NAAAAAwCSmc0AAAAAAW8FzQAAAAIBSDHRAAAAAIIlWdEAAAABAaWB0QAAAAMAqj3RAAAA=
AAH6hdEAAAABAJDx1QAAAAADEk3VAAAAAgPCxdUAAAACAKL51QAAAAAAo8XVAAAAAIJ+kdkAA=
AABgwLp2QAAAAMDAAHdAAAAAQPNBd0AAAACg7k93QAAAAMCPW3dAAAAAADBld0AAAACgvuR3Q=
AAAAED5fnhAAAAAwIXkeEAAAABgT4t5QAAAACBvjHpAAAAAwBcSfUAAAABgOpN9QAAAACDxpH=
5AAAAAgBlsgUAAAACAV8GBQAAAAADUFYJAAAAAwJYshEA=3D</data>
            </mzArrayBinary>
            <intenArrayBinary>
                <data precision=3D"64" endian=3D"little"
length=3D"85">AAAAwMPJAUAAAABArr70PwAAAMD/xgBAAAAAoH+3/D8AAACgkT4LQAAAAIC=
GFhNAAAAAIFnSG0AAAADgCTflPwAAAMAIB29AAAAA4IQHM0AAAAAg3CwDQAAAAOCtROM/AAAA=
YPO15z8AAADApR9IQAAAAICUefg/AAAAQMlXMUAAAAAg8krxPwAAAEDJavk/AAAAIAaR8T8AA=
ABAuVEkQAAAAMCItglAAAAAwGV95z8AAACAF9o4QAAAAMCmzQ5AAAAAIPfSAUAAAAAAsnwaQA=
AAAEBm+e0/AAAAgG4sAEAAAAAg0Sw7QAAAAADCngVAAAAAgFatB0AAAABA5fTsPwAAAAD2lAR=
AAAAAYFmJEEAAAADAAo4xQAAAAMBx1QJAAAAAQNaQNEAAAABgJoNTQAAAAGCvGCRAAAAAwBaG=
IUAAAABAjE36PwAAAADyNQBAAAAAoKztIkAAAACAlW/tPwAAAIBRJO8/AAAAYNy5CUAAAABAh=
iBaQAAAAIDzvgpAAAAA4BzgA0AAAADg3CbyPwAAAOB7xw5AAAAAAImSI0AAAAAgdOwQQAAAAC=
AeuPo/AAAAoGo07D8AAABg4JTzPwAAACBtRhVAAAAA4KLT9D8AAACAIQUhQAAAAODRDARAAAA=
AACjGFkAAAADApNzpPwAAAEBNTvU/AAAAIBY9CEAAAABAfF0PQAAAAGBcPx1AAAAAgDyQBEAA=
AACAMhf6PwAAAADboPI/AAAAgPUCFUAAAAAA4yA6QAAAAEDaqApAAAAAALA0BEAAAABgV+YwQ=
AAAAACdvPY/AAAAIBdaAUAAAADgLFwJQAAAAECsDQxAAAAAoDSWB0AAAAAASu0BQAAAAECuaB=
RAAAAAoN22IkAAAADAYNTxPwAAAGD5xwJAAAAAINkzB0A=3D</data>
            </intenArrayBinary>
        </spectrum>

--=20
Alexandre Masselot, phD
Senior bioinformatician
www.genebio.com
voice: +41 22 702 99 00