[Psidev-ms-dev] PSI MSS WG call notes

[Eric D. <Eri...@sy...>]

Present: Steffen, Juanan, Andy, Matt, Eric, David



Discussion of CV terms is captured below. Please let me know if there are
further comments or errors. David will follow up with a slightly more
official CV amendment proposal.



modulation time



[Term]

id: MS:1000XXX

name: modulation time

def: "Duration of a complete cycle of modulation in a comprehensive
two-dimensional separation system, equals the length of a second dimension
chromatogram, i.e., the time between two successive injections into the
second column." [PSI:MS]

xref: value-type:xsd\:string "The allowed value-type for this CV term."

is_a: MS:1000857 ! run attribute

relationship: has_units UO:0000010 ! second

relationship: has_units UO:0000031 ! minute



inlet temperature



[Term]

id: MS:1000XXX

name: inlet temperature

def: "Temperature of the instrument inlet." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000XXX ! inlet attribute

relationship: has_units UO:0000012 ! kelvin

relationship: has_units UO:0000027 ! degree celsius



source temperature



[Term]

id: MS:1000XXX

name: source temperature

def: "Temperature of the instrument source." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000482 ! source attribute

relationship: has_units UO:0000012 ! kelvin

relationship: has_units UO:0000027 ! degree celsius



[Term]

id: MS:100????

name: inlet attribute

def: "Property of an instrument inlet that needs a value." [PSI:MS]

relationship: part_of MS:1000458 ! source



+ Need to add to mzML mapping file the addition of inlet attributes,
modulation time.



SQID:



+ David will create a formal proposal of the SQID terms as suggested and
send it out for discussion/approval



Peak intensity discussion:



1) Add a “spectrum” prefix to the current “peak” terms as listed here:



 MS:1000442 spectrum

  +  MS:1000231 spectrum peak

      + MS:1000042 spectrum peak intensity (has units and value) defined
for mass spectrum

          + MS:100???? spectrum peak height (has units and value)

          + MS:100???? spectrum peak area (has units and value)



[Term]

id: MS:1000231

name: spectrum peak

def: "A localized region of relatively large ion signal in a mass spectrum.
Although peaks are often associated with particular ions, the terms peak
and ion should not be used interchangeably." [PSI:MS]

relationship: part_of MS:1000442 ! spectrum



[Term]

id: MS:1000042

name: spectrum peak intensity

def: "Intensity of ions as measured by the height or area of a peak in a
mass spectrum." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000455 ! ion selection attribute

relationship: has_units MS:1000131 ! number of counts

relationship: has_units MS:1000132 ! percent of base peak

relationship: has_units MS:1000814 ! counts per second

relationship: has_units MS:1000905 ! percent of base peak times 100

relationship: has_units UO:0000269 ! absorbance unit

relationship: part_of MS:1000231 ! spectrum peak



[Term]

id: MS:100????

name: spectrum peak height

def: "Intensity of ions as measured by the height of a peak in a mass
spectrum." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000042 ! spectrum peak intensity

relationship: has_units MS:1000131 ! number of counts

relationship: has_units MS:1000132 ! percent of base peak

relationship: has_units MS:1000814 ! counts per second

relationship: has_units MS:1000905 ! percent of base peak times 100

relationship: has_units UO:0000269 ! absorbance unit



[Term]

id: MS:100????

name: spectrum peak area

def: "Intensity of ions as measured by the area of a peak in a mass
spectrum." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:1000042 ! spectrum peak intensity

relationship: has_units MS:1000131 ! number of counts

relationship: has_units MS:1000132 ! percent of base peak

relationship: has_units MS:1000814 ! counts per second

relationship: has_units MS:1000905 ! percent of base peak times 100

relationship: has_units UO:0000269 ! absorbance unit





MS:1000625 chromatogram

  +  MS:1000??? chromatogram peak

      + MS:100??? chromatogram peak intensity (has units, etc.)

          + MS:100???? chromatogram peak height (has units, etc.)

          + MS:100???? chromatogram peak area



[Term]

id: MS:100????

name: chromatogram peak

def: "A localized region of relatively large ion signal in a chromatogram."
[PSI:MS]

relationship: part_of MS:1000625 ! chromatogram



[Term]

id: MS:100????

name: chromatogram peak intensity

def: "Intensity of ions as measured by the height or area of a peak in a
chromatogram." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

relationship: has_units MS:1000131 ! number of counts

relationship: has_units MS:1000132 ! percent of base peak

relationship: has_units MS:1000814 ! counts per second

relationship: has_units MS:1000905 ! percent of base peak times 100

relationship: has_units UO:0000269 ! absorbance unit

relationship: part_of MS:1000231 ! chromatogram peak



[Term]

id: MS:100????

name: chromatogram peak height

def: "Intensity of ions as measured by the height of a peak in a
chromatogram." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:100???? ! chromatogram peak intensity

relationship: has_units MS:1000131 ! number of counts

relationship: has_units MS:1000132 ! percent of base peak

relationship: has_units MS:1000814 ! counts per second

relationship: has_units MS:1000905 ! percent of base peak times 100

relationship: has_units UO:0000269 ! absorbance unit



[Term]

id: MS:100????

name: chromatogram peak area

def: "Intensity of ions as measured by the area of a peak in a
chromatogram." [PSI:MS]

xref: value-type:xsd\:float "The allowed value-type for this CV term."

is_a: MS:100???? ! chromatogram peak intensity

relationship: has_units MS:1000131 ! number of counts

relationship: has_units MS:1000132 ! percent of base peak

relationship: has_units MS:1000814 ! counts per second

relationship: has_units MS:1000905 ! percent of base peak times 100

relationship: has_units UO:0000269 ! absorbance unit





+ Andy will check with Martin on what to do with these. Tidy them up a
little at least:

“peak area” x2

“peak intensity”



Eric had suggested:

MS:1001843 MS1 feature height quantification (no units or value) (concept
of performing quant via this method)

MS:1001844 MS1 feature area quantification (no units or value) (concept of
performing quant via this method)



Next meeting:

- Nov 22nd 8am Seattle Time?

+ yes