Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

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

Hi Susan,

This direct infusion experiment is exactly why the 'acquisition time'
parameter in not called 'retention time'.

The individual acquisition time would start at 0 and depending on the
acquisition rate of your instrument (~ms to ~sec), the relative acquisition
time is recorded (probably as 'time in minutes') for the duration of the
infusion.

Thanks for your note - it helps to see the various ways instrumental methods
are set up.

Randy

-----Original Message-----
From: Susan M. Kennedy [mailto:Sus...@Da...] 
Sent: Saturday, November 11, 2006 10:37 PM
To: rkj...@in...
Subject: Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

Hi All
I'm not exactly sure how this fits into this discussion, but I think it is
pertinent.  We use infusion with gas phase fractionation which does not take
place in a chromatographic time frame.  Specifically we infuse a sample for
a
specific period of time (i.e. 8min) during which time the Mass Spec is
program
to only consider a specific set of ions(i.e. mz 350-450) for MSMS for a set
amount of time (ie1minMZ 450-550) and so forth up to 8min.  This is our
protocol
for routine protein ID of gel slices.

Feel free to email me if you need anymore detail

Thanks,
Susan

Susan M Kennedy
Asst. Manager for Protein Services
MB & Proteomic Core Facility

sm...@da...
http://www.dartmouth.edu/~mbcf/


--- You wrote:
Hi everyone,

Short version:

This is confusing and we need to deal with it directly in the CV.  Below is
a long discussion - the short version is that 1000038/1000039 are meant to
be relative acquisition times which in chromatography system would be
'retention time' but this is not true for non-chromatography systems, so we
need to clean up the nomenclature.

Long version:

There are two terms in the CV which are meant to represent relative
acquitisiton time from the start of overall acquisition process.  The data
type is expected to be a floating point number - not a date/time stamp.

As such, it is ideally suited (and intentionally designed) to hold a
retention time.  However, since 'retention time' is not globally applicable
to all separation methods, and since not all flow-based methods or
sequential acquisition methods involve separation at all (flow-injection,
etc.), then calling this term 'retention time' was overly specific.

For MALDI system where multiple spectra would be collected from a single
spot, the idea of recoring the time from the first spectrum acquired for a
spot seemed to match this defintion of acquisition time, and since mzData
1.05 files cannot handle multiple samples, then each spot on the plate would
get it's own mzData file whose admin description could include creation
dates and times.

As for the precise meaning of a relative acquisition time (in minutes or
seconds), we are somewhat at the mercy of the base acquisition system.

There are two time-frames which need be considered: analyzer time, and
flow-system time.

A typical analyzer takes some finite time to perform a single acquisition.
Most systems combine multiple low-level acquisitions into a single reported
acquisition (like most ion traps and TOF systems).  Some systems record the
time representing the start of an atomic operation which results in the
production of a single reported spectrum.  Other systems record the
concluding time of the spectrum.

It is not usually critical to determine if the time indicated is at the
start of the spectrum scan, or the end, since it is a very short time in
almost all systems and is consistently done within individual analyzers.

For most systems used in protoemics, there flow-system time is a completely
different thing.  In data-dependent acquisitions, there can be large
variations is the cycle-time of the instrument, so there will usually not be
a 'sampling frequency' in the usual sense - although you can configure
experiments so have s fixed sampling frequency.

This means that the acquisition time marks the time from the start of the
acquisition at which the particular spectrum is recorded.  If several
spectra are combined then you are working in flow-system time, and there are
several ways to describe what has been done.

The very best way to handle this is to use the
'acqSpecification/acquisition' elements to record exactly which acquisitions
are combined - including their acquisition times.

As for the acquitision time of the combined spectrum, it is then possible to
indicate either the start of the sequence, or, if you are processing
chromatographic peaks, you can record a peak parameter like the apex time,
or the centroid of the peak (which is what most chromatographers think of as
'retention time').

This suggests that we should have new CV terms to allow the specification of
'retention time' from the chromatographic point of view, and perhaps clean
up the nomenclature to specify that 1000038/1000039 are relative acquisition
times.  We should also consider adding a true datetime stamp CV term which
could be used to store a timestamp for the sample - especially if we move to
allowing multiple samples in a single file (proposed for dataXML).

Suggestions about additions/changes to the CV?

Randy
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