Re: [Psidev-ms-dev] Representing MRMs in mzML

[Angel P. <an...@ma...>]

don't know enough about the experiment type to give randy a straight answer,
so I'll leave that to the-folks-in-the-know. One far out idea for "saving
space" would be to define the transitions as a set of binary arrays, then
reference that as the parent spectra for any scans that use those
transitions.... But boy is that an absolute bastardization of the schema.

-angel

On 6/21/07, Eric Deutsch <ede...@sy...> wrote:
>
>  Hi Randy, one can have an array for each.  In fact, based on the phone
> con earlier in the week, I was intending to add a DwellTimeArray.
> Essentially, one can have as many arrays as needed for parameters for the
> list of transitions, as long as the definition of the array is contained in
> the CV.
>
>
>
> Another space saving feature that was discussed was not having to repeat
> those arrays over and over when they are the same. Unfortunately, the
> problem with space-saving tricks is that they can make writing and reading
> more complicated.
>
>
>
> I have yet to study the detailed emails you sent out in the last two days.
> I will get to them and they will be considered carefully next week if not
> before.
>
>
>
> Thanks,
>
> Eric
>
>
>
>
>   ------------------------------
>
> *From:* Randy Julian [mailto:rkj...@in...]
> *Sent:* Thursday, June 21, 2007 11:08 AM
> *To:* Angel Pizarro
> *Cc:* psi...@li...; Pierre-Alain Binz; Eric
> Deutsch; Sean L Seymour; Duchoslav, Eva; Shofstahl, Jim
> *Subject:* RE: [Psidev-ms-dev] Representing MRMs in mzML
>
>
>
> Angel,
>
>
>
> How would three binary arrays get to all the details (dwell time,
> collision energies, polarity, etc.)?
>
>
>
> Randy
>
>
>
> Randall K Julian, Jr. Ph.D.
> CEO Indigo BioSystems
> (317) 536-2736 x101
> (317) 306-5447 mobile
>
> www.indigobio.com
>
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>  ------------------------------
>
> *From:* del...@gm... [mailto:del...@gm...] *On Behalf Of *Angel
> Pizarro
> *Sent:* Thursday, June 21, 2007 1:02 PM
> *To:* Randy Julian
> *Cc:* psi...@li...; Pierre-Alain Binz; Eric
> Deutsch; Sean L Seymour; Duchoslav, Eva; Shofstahl, Jim
> *Subject:* Re: [Psidev-ms-dev] Representing MRMs in mzML
>
> Interesting proposition. What's the space trade-off for this approach vs.
> repeating the transitions as  three binary arrays (Precurs. Ion, Product
> Ion, Intensity) and assuming a positional relation between arrays for each
> scan (as we currently do with mzData data arrays)?
>
> I would think that the 3 array approach would use less space (than what is
> currently in the example) and be easier to produce and interpret. The only
> way I see to reduce the space would be to further group the transitions into
> sets and only reference that one annotation from the spectrum, but this adds
> yet another level of cv traversal for parsing and complexity in instance
> production, which folks seem to frown upon.
>
> example of two spectra with 100 randomly generated 32-bit double floats
> representing the transitions attached. Just the spectra though, not the full
> annotations.
>
> -angel
>