[Psidev-ms-dev] PSI-MSS WG Tuesday call minutes

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

Present: Matt, Marc, Darren, Fredrik, Eric

 

Agenda:

- What still needs to be addressed before submission?

+ Fredrik

+ Extra validation rules

+ Sample files are part of submission. So units CV must be fixed.

- Update of schema to explicit typing (no functional change?)

+ Seems fine

- Fredrik proposes a change to schema for "neutral loss / SRM scans
revisited" (01-23)

+ Fredrik will send out an example of what he thinks the SRM scans should
look like

+ Fredrik sent out an example of better way of neutral loss. Everyone on the
call agreed

+ Except replace isolation width with a lower and upper bound.

+ Approve change that Fredrik proposes.

+ Fredrik will check in xsd

+ Fredrik will update his example with lower and upper bound

+ Marc will update mapping file

+ Fredrik will email out a revised proposal for SRM scan encoding

- Problem with Thermo native ID format (01-14)

+ Definitely must be fixed. We decided to go with "controllerType=MS
controllerNumber=1 scan=1"

- ASMS abstract

+ Make sure recent contributors are on the author list

+ Discuss who is presenting author next week

- New terms: "sum peak picking" and "max peak picking" under "peak picking"
(2) (01-23)

  (or height and area?)

+ choose maximum and integrated peak picking

+ Marc will add these

- Resolve "MSn spectrum" problem (01-23)

+ Deprecate "product ion spectrum" (already synonym of "MSn spectrum"

+ Add "Nth generation product ion spectrum" as synonym to "MSn spectrum"

+ Keep "MSn spectrum" as is

+ Approve the hierarchy from Matt on 01-21 except replace "product ion
spectrum" with "MSn spectrum"

- Retention time unit problem (01-23)

+ Policy should be for entries that can have a single unit, they should have
a single unit: retention time will only allow "minute", wavelength will only
allow "namometers"

+ In a few case software should support multiple HAS_UNITS lines (so for
mass tolerance term, there would be two HAS_UNITS: "m/z" and "ppm".
Intensities should be "counts" or "eV".

+ Eric will send out an email about this policy for further haggling

- Marc suggests adding some additional units (01-23)

+ Fine, but use a single term wherever feasible. Repost.

- Issue tracker: https://sourceforge.net/tracker/?atid=1126041
<https://sourceforge.net/tracker/?atid=1126041&group_id=65472&func=browse>
&group_id=65472&func=browse

- Next call? Feb 3?

+ Yes Feb 3