[Psidev-ms-dev] multiple precursor reporting

[Eric D. <ede...@sy...>]

[Posted on behalf of Darren Kessner]

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Hi all,

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First some background - we (Parag Mallick's lab SFCAP at Cedars-Sinai)
have a tool that does a recalculation of precursor m/z values for ms2
spectra by analyzing the associated FT survey scan.  During this
analysis, we often find multiple species in a small window around the
reported precursor.  We would like to report all these precursors,
preferably with scores, for use downstream during the database search.

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Two possibities of encoding this information come to mind:

1)       Adding the multiple precursors as additional <precursor>
elements in the <precursorList>.  I'm not sure if this is the intended
use of the <precursorList>.

2)       Adding multiple <ionSelection> elements to a single <precursor>
element:

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<precursor spectrumRef=3D"19">

<ionSelection>

                        <cvParam cvLabel=3D"MS" accession=3D"MS:1000040"
name=3D"m/z" value=3D"445.34"/>

                        <cvParam cvLabel=3D"MS" accession=3D"MS:1000041"
name=3D"charge state" value=3D"2"/>

            </ionSelection>

            <ionSelection>

                        <cvParam cvLabel=3D"MS" accession=3D"MS:1000040"
name=3D"m/z" value=3D"444.00"/>

                        <cvParam cvLabel=3D"MS" accession=3D"MS:1000041"
name=3D"charge state" value=3D"1"/>

            </ionSelection>

<activation>

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</activation>

</precursor>

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Adding this second <ionSelection> element causes validation to fail with
the online validator.

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We would like to report an assoicated score with each precursor m/z
value, but I'm not sure what the preferred way is to do that.

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<ionSelection>

            <cvParam cvLabel=3D"MS" accession=3D"MS:1000040" =
name=3D"m/z"
value=3D"444.00"/>

            <cvParam cvLabel=3D"MS" accession=3D"MS:1000041" =
name=3D"charge
state" value=3D"1"/>

            <cvParam cvLabel=3D"MS" accession=3D"MS:9999999" =
name=3D"score"
value=3D".89"/>              <-- ????

</ionSelection>

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Darren

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Darren Kessner

Scientific Programmer

Dar...@cs...

310-423-9538

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Spielberg Family Center for Applied Proteomics

Cedars-Sinai Medical Center

http://www.sfcap.cshs.org/ <http://www.sfcap.cshs.org/>=20

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