Unique identifier

[michaelwitting]

What shall be the format of a unique ID in the QFeature object and for all downstream analysis?
I would argue for something like MXXXTYYYCZZZ where the XXX denotes the nomimal mass of the feature, YYY the retention time in seconds and ZZZ potentially present CCS values (make it future proof).

Example:

mz 181.070665, RT 6.73 minutes would become M181T404

What do you think @sneumann, @bitbarbie and @LiesaSalzer ?

[LiesaSalzer]

sounds good. What if there is already an ID? overwrite it?

[sneumann]

Sounds good. Only question would be whether we include a Study ID anywhere or not.
IF all our networks will ever only cover one dataset, or at least we assume that all identical MXXXTYYYCZZZ
are the same feature, then this proposal makes sense. What is CZZZ on our old QTOF ? Missing ?
C000 or CN/A ? Yours, Steffen

[michaelwitting]

@LiesaSalzer
If there is an ID I would keep it. Any objections?

@sneumann
How shall it look like with a study ID?

MXXXTYYYCZZZ@MTBLSAAAA?

If there is CCS value I would drop this part.

[sneumann]

I like the @ part. That keeps it optional, and we have a choice of MTBLS or DOI or whatever ;-) And thinking in terms of a regex, the XX, YY and ZZ would have to be numeric , in Da , sec, and angström ?! respectively. Yours, Steffen

[michaelwitting]

Yes, that is the plan!

[bitbarbie]

Is M181T404 unique enough for sensitive machines?
mz 181.070665, RT 6.73 minutes -> M181T404
mz 181.470665, RT 6.74 minutes -> M181T404
The second combination migth not be relevant, but I remember that I came cross this problem, that there were Features close by.

[rsalek]

I would think adding study ID (i.e. MTBLS) to the QFeature might be too much? Maybe some where else to capture it would be better? Header etc ...

[michaelwitting]

Is M181T404 unique enough for sensitive machines?
mz 181.070665, RT 6.73 minutes -> M181T404
mz 181.470665, RT 6.74 minutes -> M181T404
The second combination migth not be relevant, but I remember that I came cross this problem, that there were Features close by.

I think features that have the same mass should be appart by minimum one second, otherwise the would be one feature.

[michaelwitting]

I would think adding study ID (i.e. MTBLS) to the QFeature might be too much? Maybe some where else to capture it would be better? Header etc ...

It might look like a overkill, but makes the ID really unique. Even between datasets that might use the same LC-MS method and therefore have the same IDs.

QFeatures is not handling any sample headers, I think this would go to MSExperiment, right @sneumann ?

[rsalek]

I probable do not know the extend of your use case here and the details of the format. Maybe be can chat tomorrow? Just thinking keeping it simple

[michaelwitting]

On top of the discussion: How shall we call the variable? $uniqueID or $id or ???

[michaelwitting]

And another point: Shall we encode the ionization mode, e.g. POSMXXXTYYYCZZZ@MTBLSABCD

[LiesaSalzer]

And another point: Shall we encode the ionization mode, e.g. POSMXXXTYYYCZZZ@MTBLSABCD

I like the additional information about the ionization mode!

[LiesaSalzer]

On top of the discussion: How shall we call the variable? $uniqueID or $id or ???

I would say keep it simple with 'id'