Hi,
after dwelling so much about use cases, here's what I can come up with,
guessing from the schema and some of my ideas,
as a discussion base on this list and for the next telco.
Yours,
Steffen
1.3 Use cases
=============
[ - Mention TSV formats... ]
TraML is designed as a format to keep information needed to
configure and perform MS experiments. This includes SRM/MRM experiments,
especially for quantitation, and MS/MS experiments e.g. for
identification.
1) A quantitation experiment is typically performed on a set
of known proteins or compounds, and for each the instrument
measures one or more transitions (defined as precursor/product pairs)
are measured.
The definition for transitions have to be created
(retrieved from spectral libraries or predicted from sequences)
by external software. Information how those were predicted
is stored as well.
Those transitions MAY be validated (measured) on one
or more instruments, and the analytical configuration(s)
are stored with the transition.
The TraML documents can be translated into vendor-dependent
files suitable to create/configure an SRM/MRM experiment
on a Triple-Quad, Ion Trap or other suitable mass spectrometer
using external software. Ideally, the machine configuration
can be obtained or derived from the set of validated transitions.
2) A TraML file can describe an MS/MS experiment
via the specification of targets as retention time windows
and precursor mass both through inclusion- and exclusion lists.
The definition for targets for the inclusion/exclusion lists
have to be created based on a preselection of known
(un-)desired compounds or proteins retrieved from databases,
or (potentially unidentified) precursor mass and retention time windows
measured during preceding profiling experiments.
In case of known proteins and compounds, they are annotated as well.
The TraML documents can then be translated into vendor-dependent
files suitable to create/configure an MS/MS experiment
on a Triple-Quad, QqTOF, Ion Trap other suitable mass spectrometer.
Ideally, the machine configuration can be obtained or derived from the
set of validated transitions.
The list of targets is unrelated to the list of transitions,
and often only one of them is populated [True ?].
There will be limited support for the following use cases:
----------------------------------------------------------
The following use cases will not be supported in version 1 of TraML:
--------------------------------------------------------------------
- A TraML file can not describe neutral loss scans
(We don't want to have <neutralLoss> as alternative
to the <precursor><product> pair...)
- A TraML file can not describe arbitrary MS^n experiments where n >= 3.
(We don't want nested <transitions> ...)
[But actually both would be desirable for a later revision,
if TraML aims at describing MS experiments !]
--
IPB Halle AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann http://www.IPB-Halle.DE
Weinberg 3 http://msbi.bic-gh.de
06120 Halle Tel. +49 (0) 345 5582 - 1470
+49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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