Re: [Psidev-ms-dev] mzML pick file question

[Randy J. <rkj...@in...>]

Hi Henk,

mzML was designed for the application you described.  Take a look at the
specification document:

http://www.psidev.info/index.php?q=3Dnode/303

In this public comment release, the spectrum element allows multiple
binary arrays to be stored.  The main ones would be m/z and intensity.
The thought was there could be others - like picked peaks.  We have
wrestled with allowing human readable arrays and I think the group
concluded they would be too confusing.  There are many ways to do human
readable arrays and that violates the goal of minimizing 'ways to
represent the same thing' in the standard - a very good goal.

This means that you will either have to encode the peak list in binary,
or you could use either the cvParam or userParam elements.  I would
recommend that we adopt a standard nomenclature for picked peaks and
represent this in cvParams for situations where there are not too many.

The fragmentation spectra can be stored directly and are best
represented in the binaryDataArray - this is what it was meant for.  If
you have a large number of picked peaks, this binary array is also the
best way to store this type of data.

As for 'fragments' of mzML, the spectrum element does have an ID
attribute.  In theory, this means that each is uniquely identified in
the file and could be returned as part of a query (I'm thinking XQuery
style extraction from the document).  While the spectrum element is not
self contained, it is 'identifiable' so is a candidate for a return
value from an XQuery or an LSID request - I don't think we have not
gotten that far - any suggestions?

Read through the specification and let us know if you think it's unclear
on how the standard could do what you want.  We are at the point where
external readers are needed.

Thanks,
Randy Julian

-----Original Message-----
From: psi...@li...
[mailto:psi...@li...] On Behalf Of Toorn,
H.W.P. van den (Henk)
Sent: Thursday, November 22, 2007 10:23 AM
To: Mass spectrometry standard development
Subject: [Psidev-ms-dev] mzML pick file question

Dear developers,

I have some questions concerning the mzML format.
We have some collaborators who are forced to use MS-peak pick files in
order to target peaks for MS-MS in a later run. To be more clear, the
workflow would be: do an MS run, pick the peaks you are interested in,
rerun the MS, use the list of picked peaks to do further fragmentation.=20

My questions are: would it be possible to store such picked peaks in a
part of the mzML file, together with the original MS-spectra and the
resulting MS-MS fragmentations? Are there any obvious ways that
fragments of the mzML files could be used as an intermediary file
format?

Thanks in advance, Henk van den Toorn

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