animl-develop

[Animl-develop] LCMS

[Mark F. B. <sa...@co...>]

While I have Burkhard's attention...(hopefully)

(1) Is LCMS its own technique or does it reuse LC and MS? (do hybrid
techniques need their own individual definitions?)  Let's assume LCMS reuses
LC and MS.

If ExperimentStep is the application of a technique, then LC and MS Pages go
in differnt ExperimentSteps while UV214, UV254, ELS, NCLD all go in the same
ExperimentStep.

If multi-detector data goes in multiple ExperimentSteps, then how do we hold
multiple instances of that hybrid analysis in one file?

Or perhaps they shoould all go in the same Exper ExperimentStep.  Now we
have further possibilities - are these to be grouped together, entered
hierarchically in PageSet-Page-PageSet nests?  What if you have LCUV and a
series of MS spectra with no parent chromatogram? etc. etc.  Will each new
hybrid technique have to define its own way of nesting data.  Perhaps you
begin to see why I suggest we do away with nesting and use clearly defined
categories and pointers to link them together (keyrefs).

If they go in the same ExperimentStep, is there any requirement that they be
in a particular order?  Could you order them like this:
MS1, UV chromatogram, MS5, ELS chromatogram, MS2, TIC chromatogram, MS25,
XIC mz215-217 chromatogram, MS4...

Inserting data is one thing, parsing another, but attempting to hold large
datasets in memory quite another.  As a result, AnIML Viewers may have an
impossible challenge.  I would recommend that we strictly standardize the
order of elements in AnIML and also require the creation of a timeline
technique to include:

timeOffset
index
character-offsets to each Page\Vector

The last item makes viewing large numbers of spectra possible.  Without it,
AnIML is reduced to a data interchange format and cannot be viewed directly.
Which raises the question of character encoding - should we enforce Unicode
xxx...thus doubling the size of our base64binary EncodedValueSets.

I want to reduce the possible ways to fill AnIML to one.

Re: [Animl-develop] LCMS

[<Mar...@wa...>]

Hi Mark,

> (1) Is LCMS its own technique or does it reuse LC and MS=3F (do hybrid
> techniques need their own individual definitions=3F)  Let's assume LCMS
reuses
> LC and MS.
As far as I remember, we decided that we build hyphenated techniques out of
base techniques, so your assumption is correct.

> If ExperimentStep is the application of a technique, then LC and MS Pages
go
> in differnt ExperimentSteps while UV214, UV254, ELS, NCLD all go in the
same
> ExperimentStep.
This is the difficult point about chromatography: the multitude of
different detectors. I think the cleanest approach would be to make each
detector a different technique (or maybe technique extensions). This would
require to put the UV, ELSm NCLD data into different ExperimentSteps.

> If multi-detector data goes in multiple ExperimentSteps, then how do we
hold
> multiple instances of that hybrid analysis in one file=3F
Each detector-specific ExperimentStep would have a Reference element
pointing up the tree to the mother element, and would possibly sit in a
subordinate ExperimentStepSet of the mother page.

> Or perhaps they shoould all go in the same Exper ExperimentStep.  Now we
> have further possibilities - are these to be grouped together, entered
> hierarchically in PageSet-Page-PageSet nests=3F  What if you have LCUV and
a
> series of MS spectra with no parent chromatogram=3F etc. etc.  Will each
new
> hybrid technique have to define its own way of nesting data.  Perhaps you
> begin to see why I suggest we do away with nesting and use clearly
defined
> categories and pointers to link them together (keyrefs).
I see your point here. We need to put up guidelines for users how to
structure hyphenated data.

Maren.


Mit freundlichen Gr=FC=DFen / Best regards

Dr. Maren Fiege
Product Manager

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Waters Informatics
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Tel. +49 2234 9207 - 0 Fax. +49 2234 9207-99
Reply to: mar...@wa...
http://www.creonlabcontrol.com
http://www.watersinformatics.net
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Re: [Animl-develop] LCMS

[Burkhard S. <b_...@us...>]

Hi Maren and Mark,

I think Maren put this very well. A few comments:

> > (1) Is LCMS its own technique or does it reuse LC and MS? (do hybrid
> > techniques need their own individual definitions?)  Let's assume LCMS
> reuses
> > LC and MS.
> As far as I remember, we decided that we build hyphenated techniques out of
> base techniques, so your assumption is correct.

Yes.

> > If ExperimentStep is the application of a technique, then LC and MS Pages
> go
> > in differnt ExperimentSteps while UV214, UV254, ELS, NCLD all go in the
> same
> > ExperimentStep.
> This is the difficult point about chromatography: the multitude of
> different detectors. I think the cleanest approach would be to make each
> detector a different technique (or maybe technique extensions). This would
> require to put the UV, ELSm NCLD data into different ExperimentSteps.

I agree, using different techniques for each detector and putting the
data into different ExperimentSteps would be the cleanest way.

> > If multi-detector data goes in multiple ExperimentSteps, then how do we
> hold
> > multiple instances of that hybrid analysis in one file?
> Each detector-specific ExperimentStep would have a Reference element
> pointing up the tree to the mother element, and would possibly sit in a
> subordinate ExperimentStepSet of the mother page.

Correct. So each MS spectrum would have a Reference pointing up to the
time vector of the LC chromatogram page.

Have a good weekend!

Best wishes,
Burkhard