Closed GoogleCodeExporter closed 9 years ago
I actually commented back in 2011 on the retention time issue in another issue
that was set as "Fixed" so I guess nobody ever looked at it:
"Should retention time be obsoleted and replaced by scan start time? I find it
odd that mzML and mzIdentML use different terms to mean the same thing. For
mzML we agreed that retention/elution time is a peptide/compound chromatography
property, not a spectrum property."
MS:1001114 ("retention times(s)") is an isolated term created when mzIdentML
had a separate CV but was possibly kept around for use with mzQuantML as well?
I have seen mzIdentMLs using this term.
MS:1000894 ("retention time") is the root of a hierarchy of terms for TraML. It
is intended to describe peptides, not spectra. I think it is well suited to be
used in mzQuantML as well, and possibly in the peptide section of mzIdentML as
well if appropriate (but not SpectrumIdentificationResults). I don't think I've
seen any mzIdentMLs using this family of terms.
MS:1000016 ("scan start time") is the PSI-approved term for describing when a
scan started acquisition. A spectrum could be comprised of multiple scans, but
mzIdentML's SIR doesn't really care about that, so the SIR could either take
the first scan time or all of them. This is the term we use in pwiz when
converting from pepXML to mzIdentML. I still think that it's not precise (and
thus potentially confusing) to use retention time when talking about spectra.
Original comment by matt.cha...@gmail.com
on 23 Jan 2013 at 5:53
Discussed at PSI2013
Decision to make an update to the specification document, clarifying that
retention time can be reported at the <SpectrumIdentificationResult level.
We should be using the same CV terms that can be annotated on mzML spectra.
Please can someone comment on most appropriate term(s) to use, since some
search engines may be combining multiple scans - correct?
Original comment by andrewro...@googlemail.com
on 17 Apr 2013 at 1:20
I forgot to add the action item to this
ACTION: Gerhard to coordinate with mzML CV terms and make sure we can map from
SIR.
Original comment by andrewro...@googlemail.com
on 17 Apr 2013 at 1:53
Hi all,
if I understood Matt correctly, he proposes to use the same term for mzML and
mzIdentML. This means we have to change scan start time so that it can also be
used in mzIdentML to
[Term]
id: MS:1000016
name: scan start time
def: "The time that an analyzer started a scan, relative to the start of the MS
run." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
is_a: MS:1001105 ! peptide result details
is_a: MS:1001405 ! spectrum identification result details
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
Then we can obsolete the term
[Term]
id: MS:1001114
name: retention time(s)
def: "Retention time of the spectrum from the source file." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001105 ! peptide result details
is_a: MS:1001405 ! spectrum identification result details
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute
and should use the following term and it's childs only in TraML
[Term]
id: MS:1000894
name: retention time
def: "A measure of the interval relative to the beginning of a mass
spectrometric run when a peptide will exit the chromatographic column." [PSI:MS]
is_a: MS:1000887 ! peptide attribute
Original comment by germa64m...@gmail.com
on 30 Apr 2013 at 8:00
Agree with Gerhard's comment, we wish to use "scan start time" at the level of
SpectrumIdentificationResult
Potentially allow this term to be repeated with different values to allow for
case where multiple MS2 spectra have been combined - all agree?
Can discuss on today's call.
Original comment by andrewro...@googlemail.com
on 16 May 2013 at 2:45
Original comment by germa64m...@gmail.com
on 2 Jul 2013 at 3:00
Original issue reported on code.google.com by
andrewro...@googlemail.com
on 23 Jan 2013 at 3:24