Re: [Psidev-ms-dev] mzML indexing

[Kessner, D. E. <Dar...@cs...>]

Right -- that's why I included the alternative, though I could have been
less terse:

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"The alternative is to require that the <index> entries are written in
the same order as the <spectrumList> entries."

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I don't know if there is a way to enforce this...

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Darren

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________________________________

From: psi...@li...
[mailto:psi...@li...] On Behalf Of Brian
Pratt
Sent: Wednesday, January 23, 2008 11:08 AM
To: 'Mass spectrometry standard development'
Subject: Re: [Psidev-ms-dev] mzML indexing

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Hi Darren,

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I wonder about this possibility:

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<index name=3D"spectrum" >

    <offset index=3D"0" scanNumber=3D"19" id=3D"S19">3512</offset>

    <offset index=3D"2" scanNumber=3D"23" id=3D"S23">16217</offset>

    <offset index=3D"4" scanNumber=3D"25" id=3D"S25">17258</offset>

     ...

  </index>

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If the response is "well, that's not legal, the index values must
increase in increments of 1 starting from 0" then I don't see why it's
needed in the first place - I'd expect that the index would just get
snarfed up into an array and you'd access the nth element to get info on
the nth scan appearing in the file.  And if it is legal then I don't see
what it's for... =20

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Brian

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________________________________

From: psi...@li...
[mailto:psi...@li...] On Behalf Of
Kessner, Darren E.
Sent: Wednesday, January 23, 2008 10:33 AM
To: Mass spectrometry standard development
Subject: [Psidev-ms-dev] mzML indexing

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Hi all,

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There are three ways to refer to a <spectrum> element -- by zero-based
index into the <spectrumList>, by 'scanNumber', and by 'id'.  However,
the <index> currently only contains scanNumber.  I would like to encode
the zero-based index and the id as well in the <index> as follows:

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  <index name=3D"spectrum" >

    <offset index=3D"0" scanNumber=3D"19" id=3D"S19">3512</offset>

    <offset index=3D"1" scanNumber=3D"20" id=3D"S20">16217</offset>

     ...

  </index>

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Including the zero-based index is important to enable random access to
the mzML file when you don't know what scan numbers are contained in the
file.  The alternative is to require that the <index> entries are
written in the same order as the <spectrumList> entries.

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Including the 'id' in the <index> entries is necessary for efficiently
dereferencing a "spectrumRef" (e.g. in <precursor> element).  Without
this, a dereference requires reading through the <spectrumList> to find
the right 'id'.  This info could be read once and cached, but this still
defeats the purpose of indexing.

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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/

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