MS2 analyzer type and fragmentation energy

[lisavetasol]

1. For some Orbitraps it's possible to measure fragments in the ion trap or the Orbitrap. It would be nice to add this information (probably next to the comment [instrument]). It may be a bit redundant since there is information about fragment tolerance, but an explicit "MS2 analyser type" column would be a more straightforward characterization of the experiment.
2. There seems to be no way of specifying HCD/CID energy. Since some tools can predict fragmentation spectra for particular energy, this parameter may be helpful with in silico libraries for DIA and different dot product scores.

[ypriverol]

1. For some Orbitraps it's possible to measure fragments in the ion trap or the Orbitrap. It would be nice to add this information (probably next to the comment [instrument]). It may be a bit redundant since there is information about fragment tolerance, but an explicit "MS2 analyzer type" column would be a more straightforward characterization of the experiment.

• @lisavetasol in the ols, you can check under mass analyzer all the possible values mass analyzer. Those that make sense? Some examples:

• time-of-flight

• quadrupole

2. There seems to be no way of specifying HCD/CID energy. Since some tools can predict fragmentation spectra for particular energy, this parameter may be helpful with in silico libraries for DIA and different dot product scores.

In the ols two terms can be use to define energy:

• collision energy
• activation energy

Please, if you think one of these is the appropriate terms let me know. I can add that to the documentation. AS I said before these terms (columns) should be optional (RECOMMENDED).

[lisavetasol]

@ypriverol

1. these mass analyzer type values look good, but the issue is that it should be possible to specify different mass analyzer types for MS1 and MS/MS spectra.
2. I think collision energy is the right term, but there should be also normalized collision energy since most of instruments measuring it not explicitly in eV, but in NCE.

[ypriverol]

@ypriverol

1. these mass analyzer type values look good, but the issue is that it should be possible to specify different mass analyzer types for MS1 and MS/MS spectra.

• You would like two columns?:

• MS1 mass analyzer type

• MS2 mass analyzer type

2. I think collision energy is the right term, but there should be also normalized collision energy since most of instruments measuring it not explicitly in eV, but in NCE.

• Lets use comment[normalized collision energy]

[ypriverol]

@lisavetasol In the normalized collision energy what will be the structure of the value? A Number, a Number with a unit?

[lisavetasol]

@ypriverol

You would like two columns?: MS1 mass analyzer type MS2 mass analyzer type

Yep, sounds perfect.

Lets use comment[normalized collision energy]

But sometimes collision energy isn't normalized. I think instead of making two comments, it may be better to make one, [collision energy] with possible units "NCE" and "eV", so the first one would be for normalized collision energy and the second one for non-normalised one? And then the structure will be a number and unit.

[ypriverol]

New CV Terms in the PRIDE Ontology:

id: PRIDE:0000544
name: MS1 mass analyzer
def: "MS1 mass analyzer" []
is_a: MS:1000451 ! mass analyzer
created_by: yperez

[Term]
id: PRIDE:0000545
name: MS2 mass analyzer
def: "MS2 mass analyzer" []
is_a: MS:1000451 ! mass analyzer

Created

[lisavetasol]

Is there a way to specify fragmentation energy in an annotation? Should I just use comment[collision energy] and fill it with e.g. '28 NCE' / '20 eV' ?

Update: found it in the "major changes #214 " with exactly this way to specify it.